Sure, and none of that has anything to do with what's "canon", since people decide for themselves what's canon. Blomkamp's movie could end up sucking and we'd be right back where we started. If some people choose to take "everything" as canon, that doesn't change anything and it shouldn't affect you at all, and if it somehow does then that's something you have to come to grips with on your own I guess. Saying, "Oh boy I hope those people who take everything as canon are presented with a scenario where they HAVE TO CHOOSE!" just makes you seem petty and juvenile.
Countless people disregard stuff even if it's on some fan-run wiki because they choose to. Colonial Marines may be "officially" canon, but I'm very sure the number of people who actually accept it as such is very, very low. Even if Blomkamp's movie undoes Alien3, Colonial Marines will still remain on the Alien wiki, and it'll still be "canon", it'll just get a footnote that it's part of some "other timeline" along with Alien3.