Do you think she could do a season 12 if Chris was fired?

I don’t think that’s even a question. Fox can’t fire Chris but they could give him a lot of money to buy his rights and produce the franchise without him. That’s what they should have done after season 10, tbh.
But yes, somehow, if Chris was out and if Fox was up to completely rebrand the show and make it a modern one, then I think she could consider it. Thats a lot of ifs, though…
Honestly, I hope they’re not going to try making a season 12 without her. In the era of Game Of Thrones, TGIT and the hundreds of shows I could quote that are a hundred times betterly written, directed and yes, acted than XF, it seems pretty pointless to keep trying to make good ol’ X-Files. I’m sure Chris Carter never watches anything else than his old own episodes and has no idea what good tv looks like in 2018.
So take him out, put a fresh showrunner, hire some new talented writers and directors who are actually able to give the show a second wind, who can be inspired by what works without badly copy/pasting (ahem, Black Mirror, ahem) and then Maybe the two lead actors will be interested in it and Maybe, maybe it’ll gather a new audience and raise up the ratings.