Let's just not forget that, although Vivienne is right about this being the worst possible time for rebellion of the Mages, that the Circle system is something that needs change, and it's something that needed to change a long time ago, but people were too busy playing police to actually do something.
It didn't change, because as with everything else, in order for it to change, both parties had to agree. It took a rebellion for the Chantry leaders to accept negotiations, and in the past, when people asked for more freedom, it did not end nicely.
There's no way to sugar coat this, this rebellion will do more harm than good, but there is blame on both sides because, the Mages might indeed be selfish - and naturally so, everyone would want their freedom in their place, and would bypass logic because of strong feelings from oppression-, but the other side would not just agree for more freedom to exist, or even worse, for the Chantry to be separated from the Circles.
I do think, this was inevitable, when you opress people for whatever reason, (self) justified or not, it is going to bite you at some point.
This could have been averted by people standing in a nice room to negotiate. Did we need 1000 years and a rebellion at this point for it to happen?
I can't help however, but wonder why did it happen now? It was SO damn convenient to have both parties to negotiate at the same spot. And suddenly, their Heads are all dead. Coincidence? I think not.
Someone took advantage of it. Why wait for a rebellion though, instead of just blowing them up at a simple negotiation, before a rebellion? I guess, because if a rebellion started, many would die from both sides, and their ranks would be decimated. Less forces to worry about?
Maybe, a group was influencing both Mages and Chantry, to make things lead to this. Could this have something to do with the people that caused this?
I don't know, but it's my conspiracy theory /tinfoil hat on.