If you have a relationship with IB and choose the Qunari, doesn't he basically acknowledge that he will eventually be called back, sent to the re-educators, and forced to forget you and his feelings for you?
...Ick.
So, yeah, that's the real reason I choose the Chargers: because even if IB follows the orders and becomes 'Hissard' truly, he's going to be brainwashed again because he's become too different then the ideal follower of the Qun. And I'm not having one of my 'inner circle' go through that, be it because he's a love interest/a friend/much more useful close to me then against me. Even if I'm playing pragmatic/occasionally jerkass inquisitor, it suits my inquisitor's purpose better to have someone loyal to them (and indeed, if you befriend Bull and save the Chargers, at the end he's like, 'Yep, we're sticking around') then to have a wild card they'd let get close to them and then be thrown away.
In other words, when choosing between people who are eventually going to turn against you (the Qunari have made no secret that yes, they are going to conquer Thedas again (or at least attempt to)) or someone (and their mercenary group, which does some decent jobs) who is loyal to you and willing to stay around and keep being loyal, it's better to take the safe bet and involve giving any advantages to the group that is and will be an enemy. As Alistair and Anora can still be part of war table missions after the whole mess with the Qunari (such as the peace negotiations with Orlais), it's safe to assume that at least the royalty survives any firebombing that may happen by the Tevinters (if it even does happen when you don't ally)- and, well, if Denerim gets destroyed by the Tevinters, it makes it easier to rally Ferelden to your purposes.
On the other side of that, looking at from a character who's not concerned about results, but about the fluffy feelings and friendship and happiness... it's actually a bit harder, as that character goes in to the alliance all 'YAY LET'S ALL BE FRIENDS' rather then the 'Okay, how can this be used to my advantage?'. However, it's the Qunari who order your army (paticularly the Blades, who are RIGHT THERE and accustomed to blending along the Coast) to stay back and gave extremely bad intelligence on that round So going between people who give bad intelligence when I'm specifically allying with them for their intelligence versus people who apparently beat up Envy on nightmare mode when he makes me cry usually (why they can't take down a few Vints is an eternal mystery of plotholeness, as Envy is a lot meaner then those Venatori) and have already offered me the fluffy feelings of friendship, I'll go with the fluffy friendship.
...This is not to say I haven't done the Qunari line, because, interesting! (And maybe Tallis.) But I find it hard to ally with them: the combination of stupid intelligence when they're trying to dangel their intelligence network in front of me as their 'bribe'/alliance trade as well as the lack of connection and eventual brainwashing of someone who's been private to my character's private decisions makes most of my characters nervous. Also, Krem is cute and there's a nice song. Qunari don't seem to sing much. I'll go with the singers. /musically inclined