Not anything. They can't go against what was said in Fallout and Fallout 2. They confirmed they see them as canon and the High-Level Events of Tactics as well. They can only debunk the Bible if they wish to do so.
Still I agree it doesn't mean it is a good call to do so.
Sure they can. By just going against them and stating that as canon. Turning coats isn't a new thing. If they want, they can turn it all from Fallout to Fallout New Vegas to some poor sods comatose dream. This is particualrly what scares me about the future titles, Beth not exploring the existing setting but turning it to another being (like partly done in the the MZ).
And to press it, it is not a good call, not even a remotely decent call. It'd be straight up full of [censored] and everyone'd know it -- even the bethfans (though they wouldn't likely care as they'd get a beth game nonetheless).
Now, I'm pretty sure that ain't gonna happen, so my troubles of the future li elsewhere. But you never know.