I suspect the hatred comes only from meta-gaming of those familiar with books and the history of inconsistency of the character treatment from developers.
First of all, Fiona is the biggest MarySue of DA universe. She happened to break every rule of the lore with zero explanation (or close to zero in some cases). She just happened to be cured from blight, get pregnant while still "greywarding", meddling in politic left and right, being personally involved with every important person in Thedas, become the most powerful mage in Ferelden and so on, and so fort. Now, last drop for some become a sudden confirmation of her being Alistair's mother, while before writers were swearing on their graves she is not (and DAO confirmed it by everything but DNA-test).
To be fair, if meddling in politics left and right and being involved with every important in Thedas is criteria for a Mary-Sue, then how on earth does that not discount Leliana or the Warden from being also two of the biggest offenders in the entire franchise?
For Leliana, she's able to survive death with a very sketchy handwave in Inquistion, became one of the prime movers and shakers for Divine Justinia, has appeared in all three games and four DLCs thus far, while also being one of the most Blight-resistance specimens encountered from Alexius' research in the Dark-Future Redcliffe?
Likewise, the Warden has meddled in politics and played Kingmaker for two different nations (Ferelden and Orzammar), if a mage was Irving's best student and one of the most powerful and influential mages in the country, has met numerous important figures in Thedas, can survive fighting an Archdemon and become the first known Warden to do so, can father an Old God Baby, and finally is looking for a cure for the Taint if alive in Inquisition?
As for the Alistair's mother part, it was heavily implied in the novels that this was the case and the supposed story in-game was vague enough that one could easily see it being manufactured to hide both Maric's elven lovechild (a major scandal if known) and a potential heir's elven heritage? Maric having knocked up a servant who died in childbirth, is far less to raise eyebrows than him admit that if anything happened to Cailan, his kingdom could potentially fall to the son he had with an elven mage and former Grey Warden.
Now, suddenly that semi-god figure were diminished to an insignificant idiot who, nevertheless, managed to sell free mages to Tevinter (and they somehow accepted it practically without a fuss - just imagine someone telling you "oh, btw, I arranged on your behalf selling you to slavery. You are welcome". Or may be that was a demonstration of her incredible power?).
Except that the Rebellion was sadly failing by the time the game is set. They've already lost Andoral's Reach and even with Alistair (or Anora) offering them safe haven in Ferelden, the Templars have continued their assault against them and have basically gotten them trapped in Redcliffe for the time being. Fiona even says that they feared that the Templars were about to kick down the door and kill them all when the Tevinters showed up and offered aid?
Secondly, while Indentured Servitude is technically a form of slavery, it's hardly uncommon in Thedas from what we've seen already. Hawke and their sibling were forced into it in DA2 to pay back the debt of getting them into Kirkwall and their reaction to Gamlen saying essentially what you wrote, was similar outrage and indignation. But because they were desperate, went along with it, just like the mages in Recliffe did.
Fiona might have screwed up by letting Alexius take control out from under her and having not necessarily consolted everyone before agreeing to Alexius' offer, but considering how screwed they were, what else was she supposed to do?
And the terms he offered were somewhat fair; none of them would be pressed into military service, at the end of ten years they would become full citizens of the Imperium (and as mages, be able to gain political power) and as contract slaves they would be like Krem's father, publicly-owned and thus afforded some respect and protection as wards of the state, unlike the non-contract slaves who typically are taken by slaving parties from other countries, who have little-to-no rights whatsoever?
It wasn't really Fiona's fault that Alexius decided to pull a Vader and renegotiate the terms of the deal, knowing that they were so desperate, they wouldn't dare object least he alter the deal and screw them over any further?