I think that if you're having to resort to mind control plots to manipulate the story into having any sense, then IMO, that's evidence of a shallow, poorly-constructed conflict, especially given that Bioware has a precedent of attempting to tackle far more complex problems than that. To me, it is preferable and sufficiently believable that people in power would make bad decisions. Everyone I know IRL has stories about "how did this moron become the supervisor" and similar stories.
IRL I have a manager that has no business being a manager, so yes, I can relate.. to a certain extent. But this goes way beyond that. Fiona couldn't have done this entirely by herself, she had to have the support of at least enough of the higher ups in the rebellion or whatever she agreed to wouldn't be worth the paper it was written on, and frankly they stand to gain pretty much nothing from this alliance. It simply doesn't make any sense to chalk this up to a bad decision, because this decision isn't "bad", it's completely nonsensical. They are selling themselves into slavery and they are not even getting a modicum of security for it, if anything they are making their own situation 1000 times worse and that's under the most ideal conditions.
I think part of the problem here is that perhaps some folks haven't really thought through the logistics. Alexius couldn't have brought much of a force with him, even something in the 50 range would probably be pushing it. He's in a foreign land, far from home and he does not have the support of the entire Imperium here, not by a long shot.
Even 50 is going to attract a great deal of attention and probably lead to him having serious problems and anything more than that would probably be seen as an invading force and dealt with long before he ever got anywhere near Redcliffe. So he can't really be bringing in much as far as forces or support is concerned. Really his nnly barganing chip would be "citizenship" in the Imperium and thus a safe haven from the Templars. But there is one monster problem with that idea, that only does the rebels any good if they can get there.
So Alexius shows up, and convinces them to sign on in return for citizenship - and then takes over Redcliffe Castle. Game over for the rebel mages, right there. No chance in hell they are ever going to make it to the Imperium, because the moment they leave Redcliffe they will not only have the Templars to deal with but more than likely an extremely hostile Fereldon army as well. No way your moving a group of refugees through that much hostile territory with that many determined enemies hunting you with every thing they have, even with a couple of dozen Venatori to bolster your ranks. Fiona and her people would have to know this, and if they are outmatched by the Templars already again a small band of Venatori aren't really going to be much good. Alexius just couldn't bring a big enough force to help protect them even if they hadn't just seriously ticked off the rightful rulers of Redcliffe by agreeing to support a hostile foreign power in their takeover of the castle.
The point is, there is really nothing in this bargain for the rebel mages to make them want to agree, to any of it. This whole thing stinks to high heaven for them, and they would know it from the outset. So yes, if there were something here that Fiona stood to gain from this bargain or at least it looked like she might be getting something, then maybe this would make sense. As it stands, it makes no sense at all. This isn't a bad decision, this isn't even a moronic decision, this is a decision that is so totally off the wall that no sane person would make it.