Oh, yeah, definitely. 
And I fully support Meredith being much, much more gentle than people assume. Even siding with the mages, Meredith never came across as HORRIBLE other than when the Red Lyrium started to really affect her.
(Have I said I love Meredith? Because I do!)
I think Meredith would have come down hard on any abuse going on she actually knew about, which is why I fully believe the corrupted Templars kept it under better wraps than assumed. Hawke just needs to know all the things so the player knows all the things.
Yes, I highly doubt that Meredith and Cullen would have let Ser Alrick and other templars abuse the mages. If Meredith was hard on the mages, I can only imagine her being even harder on her templars--because they are supposed to be the very best and take their duty seriously. Honestly, what might of been a better solution to the Kirkwall problem would be reassigning Orsino and/or/both Meredith to other Circles (different other Circles)--but then we wouldn't had much to do at the end of the game 
You can kind of see a softness to Meredith at times, especially in the Act 3 opening when she says "I know and it pains me" or something to that effect. She also asks Hawke to give her another solutions which of course Hawke can't do. I think maybe that why Cullen was sent to Kirkwall--perhaps, Meredith also has a bad experience at a Circle similar to Cullen in Origins and thought Meredith could guide him. Unfortunately, I think Meredith got a taste for power and that combined with her experiences and the idol turned out poorly. I wonder if Red Lyrium has an effect on mages at all? Also, Cullen and the other templars and mages must of had good resistance to not be affected by Meredith's sword as I am sure they were often around her. I think Cullen noticed the change in her as you get to Act 3, he starts to have doubts about Meredith compared to Act I?
I'm hoping Cullen talks about how he was sent to Kirkwall with the Inquisitor--could be a good opportunity to learn more about Meredith as well as Cullen.