***spoilers and crazy talk Ahoy!***
The dialogue with Alistair (or rather, one instance of it, since I think he has a couple of places where he'll offer the explanation about Redcliffe/Eamon/Isolde) is
Warden: So you said this Arl Eamon raised you?
Alistair: Oh, did I say that? I mean that dogs raised me. Giant slobbering dogs from the Anderfels. A whole pack of them of them, in fact.
Warden: Really? That must have been tough for them.
Alistair: Well, they were flying dogs, you see. Surprisingly strict parents, you see, and devout Andrastians to boot. Let’s see. How do I explain this. I'm a bastard and before you make any smart comments, I mean the fatherless kind. My mother was a serving girl in Redcliffe Castle who died when I was very young. Arl Eamon wasn't my father, but he took me in anyhow and put a roof over my head. He was good to me, and he didn't have to be. I respect the man and I don’t blame him any more for sending me off to the Chantry once I was old enough.
Warden: He wasn't your father? So you know who he is?
Alistair: I know who I was told was my father. He died even before my mother did anyhow. It isn't important. Arl Eamon eventually married a young woman from Orlais, which caused all sorts of problems between him and the King because it was so soon after the war. But, he loved her. Anyhow, the new Arlessa resented the rumors that pegged me as his bastard. They weren't true but, of course, they existed. The Arl didn't care but she did, so off I was packed to the nearest monastery at age ten. Just as well. The Arlessa made sure the castle wasn't a home to me by that point. She despised me.
Warden: What an awful thing to do to a child.
Alistair: Maybe. She felt threatened by my presence. I can see that now. I can’t say I blame her. She wondered if the rumors were true herself, I bet. I remember I had an amulet with Andraste's holy symbol on it. The only thing I had of my mother’s. I was so furious at being sent away I tore it off and threw it at the wall and it shattered. Stupid, stupid thing to do. The Arl came by the monastery a few times to see how I was but I was stubborn. I hated it there and blamed him for everything, and eventually he just stopped coming.
Warden: Are you sure he isn't your father?
Alistair: Yes, I am quite sure. At any rate, I don’t look anything like him. You’ll see for yourself. Not that it stopped the rumors any. All I know is that the Arl is a good man and well loved by the people.
With some bolding for emphasis (and because I like bolding).
While I do think Alistair can be a very unreliable narrator at times, I’ve always accepted his dialogue on the situation at Redcliffe at face value, since he is quite specific about the sequence of events and the cause/effect.
A few random thoughts on this... 'soon after the war' could mean almost ANYTHING, given that even 30 years later, some Fereldans are still talking as if the occupation only ended yesterday. And immediately after 'the war', Eamon was still very young. Let's see... in 8:99 Blessed, Eamon is just 15. (The Stolen Throne, pp 259 of the print edition.) Isolde is clearly even younger than he, and probably not of an age to marry immediately following the end of the Orlesian occupation.
As an aside, I find it very interesting that Connor’s birth would have come right about the time that Alistair was banished to the Chantry. (Connor is about 10 years of age. Alistair was sent to the Chantry at age 10. Alistair is 20... less 10.... carry the naught and... yup. Alistair got the boot right around when Connor was born.) My theory *Miss Ann Elk voice* as to why the boy was sent to the Chantry (and not to Rainesfere, or squired out to another lordling), that Isolde's discomfort with/dislike for Alistair had nothing to do with a belief that he was Eamon's bastard (or even rumours to that effect). Rather, I think it's possible that Alistair was banished to the Chantry because Eamon (and Isolde) knew the entire truth about Alistair's parentage... including that his mother was a mage. Magic is hereditary. (Magic being hereditary is something Isolde is quite familiar with, as she tell the Warden when offering a reward (an Enchanter's Staff) for saving both her and Connor: This staff belonged to my grandfather. He was a mage, as well. Connor no doubt owes his abilities to him.) The games strongly suggest that magic often manifests itself in a child near puberty... as it did in Isolde's own son, for example. (I have a hard time believing that even Maric the Shirker would be so irresponsible as to not reveal at least that Alistair’s mother was a mage when he farmed him out. Or that Eamon would have hidden that from his wife... though the Guerrins admittedly are not poster children for familial openness or honesty. :-/)
Anywho... as the child of a mage, there was the strong possibility that Alistair too, might possess magic. New parents want to protect their perfect new family from threats. In Thedas, a mage, or even a possible mage (and especially an untrained mage), is regarded as a threat.
The Chantry, of course, was best placed for damage control should Alistair take after his mother... toss him in the Chantry-controlled Circle, and no-one is the wiser. And when it became apparent he wasn't a mage, the more interesting 'plan B' of forcing Alistair onto the Templar path results in the Grand Cleric (and to a lesser degree, Eamon) holding sway over the person who was second in line for the throne.
This, I think, explains why the Grand Cleric was furious when Duncan conscripted Alistair (who she clearly DID 'value highly'). Imagine if Cailan were to die at some point after Alistair took his vows, or, as he did, at Ostagar. The Grand Cleric could have put forward Alistair for the throne, and who would have dared question the veracity of that claim? Especially if Eamon could offer some proof of it? And what could be more advantageous for the Chantry (and an allied Eamon) than to have a lyrium-addicted ex-Templar king as their puppet? Win-win, for the machinating opportunists!
And since Alistair insists he was not taking lyrium (and he wasn't getting any from my Wardens) I like to imagine that his innate Templar abilities are a combination of mental discipline and low-level magical acumen. (Or the latter + that uber sexxy Theirin dragonblood amiright?) Also explains his weird fascination with magical trinkets, sez me. (Because that wasn't a big a hint as to who his mom is or anything. /snark)
Finally, and even more OT but what the heck in for a copper in for a gold, what absolutely infuriates me to the point of incoherence is that Maric (who I truly believe did not give a single thought to his second son once he’d dumped him on Eamon) has been “dead” for FIVE YEARS when the Blight begins. Cailan and Anora are clearly NOT on the baby train (hence the Eamon/Celene intrigue revealed in RTO). Ferelden has for YEARS been one heartbeat away from exactly the succession crisis Cailan’s death at Ostagar precipitates. Yet Eamon, and the Chantry, (and Cailan, if I’m going to point all the fingers) have done NOTHING to prepare Alistair for “what might happen”. What could and did happen, in one heartbeat. *wordless fury*
So, tl; dr summation time for Wall o' Text and even I'm bored with what I wrote by now. IMO, the timeline seems to support that Alistair came first, Isolde came later. What anyone knew and why they did what they did is anyone's guess. My guess comes with bonus black helicopters, a double-thick tinfoil hat, too much coffee, and intense Alistair feels. Also, spellcheck wants to change 'Guerrins' to 'Guerrillas'. Which is the REALLY important bit of this post. Or something. And of course with apologies for the meander-y digression, but for me, it's all one thing. *remembers the bad stuff that happened on Tumblr when I said this and laughs maniacally before hitting the 'post' button and I'll probably delete this as soon as I'm really awake*