WARNING! THIS IS A REALLY LONG POST! YOU HAVE BEEN WARNED!
With my track record in this thread this will likely be overlooked by everyone. Much sadness occurred.
In a shoddy, hastily written prequel novel that you don't have the time or budget to give a proper editing cycle towards, you present a completely incompatible set of circumstances.
You then choose the latter as your official canon.
And what's the gain? Alistair's mother is a poorly written character who he has a good chance of never meeting? How does this enhance the story?
It enhances the back story of the world. The Dragon Age universe did not begin on 9:30 Dragon on whatever month all of the Origins occur. There are characters going through various stages of their life in the game, and they deserve an enhanced description besides a short blurb. The novels presents us the character of Maric, and what happened to him before he "died". Loghain is also enhanced in the novels as we are able to see what actually drives him, where he got his preconceptions of Orlesians and the Wardens. This is of course far better than the few lines Simon Templeton utters IF you decide to spare him in Origins.
I am also intrigued that you are saying that The Calling was poorly edited etc simply because you dislike it. Shockingly, the two are not always linked together. If you do want an example of a poorly edited book in the DA universe I will happily point you towards World of Thedas... 
It's been a while, but does he actually say that he loves this woman who he knew for all of a month? This woman who spent that entire time radiating hatred in his general direction?
Which is another problem I had with it; their "romance" was the most bile inducing, poorly written piece of sh*t excuse for a love story that I have ever had the misfortune of reading. These two people have no chemistry, no common ground, no connection. One spends the entire novel hating the other until her child hood trauma is healed by his magical penis. It's insulting drivel with nothing resembling real human emotion to it.
There is ample psychological research that shows that when two people go through extremely stressful situations that they will grow closer together (emotionally/physically) regardless of their initial feelings. It's also why men try to take women they are interested in to horror movies (this is applicable to all genders) because it increases the male's chances of getting laid. It's also why when people go to war they end up extremely close (on an emotional level) with the people that they shared the same experiences with.
So you are wrong in saying that Maric and Fiona have no connection. They have a connection and it's that they are thrown into a situation that went horribly horribly wrong. They also have a common ground in that they kind of want to live. Is it a horrible romance for entertainment purposes? Of course, and that's because it is also shockingly real. However, you can argue over whether their feelings are real or are artificially created by their situation. Although one could also argue that if the feelings are still present X amount of time after the experience then the feelings become real.
Shockingly, not all relationships are:
Person X: "We have xyz in common! I LOVE YOU!"
Person Y: "I LOVE YOU TOO!" *happy ending*
There are NUMEROUS examples of two people that seem to have no connection with each other ending up together. Is it really common? Hell if I know, I'm not interested in studying it. Does it always lead to a good, long lasting relationship? Of course not. The fact is, that it happens and as such is an example of a real relationship no matter how much you want to kick and scream and cry about it.
I'm tired of seeing people go "I don't like it, therefore it has no basis in reality" for relationships.
And another thing; Loghain was not speaking about things second hand or making assumptions. He didn't say "Well the way I heard it was" or "If I had to guess, I'd say". He speaks in a very "This is how it was" manner. As if he was there, as if he witnessed the events, as if he was consulted on them.
You can try and rationalize it away by saying that he's now retroactively speaking in assumptions, but as written in Origins, he wasn't.
Loghains character throughout the game speaks in a "This is how it is/was". It is consistent for his character to say things in that manner, and he NEVER deviates from it.
He specifically says the boys in the chantry either ignored him for his bastard status, or thought he “put on airs” and so presumably weren't kind to him.
You learn little of his time at Eamon's – other than Isolde made him very unwelcome and he slept in the stables. The last time Ban Teagon saw him he was covered in mud. Possible mixture of neglect and in addition wilful hostility from Isolde. You don't get the impression he was happy, just grateful.
Yet, and here is my point, despite this unhappy backround, Duncan and Maric were keeping an eye on him? Well they did a really bad job, Duncan only turning up at the last minute after Alistair had been desperately delaying his vows - to save him from becoming a drug addicted templar at the age of 20. Dramatic timing certainly.
And sorry about your recruitment Alistair, it wasn't Duncan taking an interest in you for you - just something else that happened to you because of your parentage. Yes, Duncan knew who you were all along.
It's either just not convincing or cheapens the narrative in Origins imho.
Just because Duncan said he would monitor the child does not mean that he has to be directly involved in his life.
Duncan may have had ulterior motives for recruiting Alistair, but does Alistair have to know in DAO those exact reasons? Does Duncan have to go all Darth Vader on Alistair? What purpose would revealing all of that to Alistair serve? What purpose would allowing the player in DAO reveal this to Alistair serve?
Expect this piece of lore to get retconned as soon as some important writer wants to write a story which would necessitate it.
Just because the writers do not decide to inform us of every single piece of lore in the DA universe does not mean that they are "retconing". That term has about as much reliabilty as "Mary Sue" when it comes to a piece of fiction. If you don't like something it's immediately a "MARY SUE!" or "RETCON!" depending on the context.
The only real "retcon" in the DA universe that I am familiar with (that is purely a retcon) is the whole Leliana debacle in DA2. Then again, that's also the problem with involving CHOICE in a game, some people are just going to get burned.
Hell...it's not like this is Star Wars...