Very interesting theme you’ve got going on there. Sounds like something I’d be interested in reading.
I’d assume Twilight would first go with the moral impulse: covering up the past is wrong, and knowledge is good, so she should not censor the ponies.
Then, because it won’t be that simple, ponies become violent in some fashion. Twilight realizes she has to do something, since her words about addressing the past and moving on aren’t getting through. But she’s not going to censor Equestria’s history, so she has to try another solution.
Whatever she comes up with has to be big enough to reach others, and it’s not going to solve the conflicts overnight. After all, they might be old wounds, but they’ve only recently been rediscovered.
It’s never been my strong suit, but I wish you luck in plotting.