Exactly, the Mages gain nothing by attacking Haven, which would only further harm the already poor image that people have of them?
Launching an assault against the people who just saved Thedas from being swallowed up by a giant hole in the sky, is such a daft move, who would ever willingly agree to it, unless they were being manipulated or controlled in some way?
The mages were always manipulated- in large part because Fiona is an idiot and a very poor leader. I don't think anyone denies this- most arguments simply quibble over whether Fiona being manipulated into making consistently bad decisions is considered the damning sin or a valid excuse.
Even if they feared the Inquisition having a Templar army at their disposal, that army currently consists of recruits, a couple squaddies and a scant few officers, who managed to escape most of the order being wiped out at Therinfal or turned into monsters?
Furthermore, Templars are either disbanded, conscripted or joined as allies of the Inquisition, so at least two of those three basically neutralised them as a threat to the mages for the time being, while the other has them being reigned in by the Inquisition?
So far, taking care of the Breach, closing Rifts and fighting demons is all the Inquistion cares about, not the Mage Rebellion. Given that Rifts are everywhere and demons are far bigger threat than the Mages, the Inquisition has far more work to do than deal with them and realistically, that gives the Mages a lot of time to weigh their options and figure out what to do next?
Launching a suicidal attack only weakens their cause, what would be the point?
The point is that Fiona and the mages have been notoriously shortsighted and unable to think things through to the logical conclusion in the past, so it's really not that surprising or different from the daft things they've done before. This is, after all, the woman who nearly got her own independence movement stillborn and locked away in the place of their declaration because she didn't have a better plan than 'hope the Divine does something she doesn't have to.'
By the time the Breach is sealed, Corypheus's cultists have effective control of the information and options of a mage polity that is notoriously culpable to being led by the nose with dissent bullied into going around. Leading the mage collective into a rebellion it consistently refused by making it believe it's back was to the wall and that it had no choice was Fiona's own strategy, after all. After that, the mages who didn't flee never seemed to actually assert themselves much in definace of 'their' leaders: they went along with the Tranquil massacre as dozens (hundreds?) of their fellow Circle refugees were systematically slaughtered, those that weren't eager supporters of the Tevinter deal sullenly went along with it, and when the castle coup was carried out we see and hear mages talk about how bad it was and how someone should do something about it... but never hear of any significant mass resistance or dissent to an option that, as soon as they occupied the keep rather than flee, was practically a death sentance on them.
Drinking the Corypheus coolaid? Duped into even more outrageous and unfounded fears than the ones that they sold themselves into slavery for? Really bad planning worthy of a Darwin award?
Not that out of character, honestly.