But that's not what they're doing at all, especially since they didn't say Alien3 sucks.
As mentioned, they pointed out significant flaws - the mystery egg out of nowhere is a flaw, and it's one that has bothered both fans and casual audiences for literally two decades now. Addressing it in some fashion isn't a bad thing. It's not like they're going to retcon out Hicks' death and have him blasting away Aliens or something.
QuoteStuff like that alienate them from a large portion of the Alien fan-base
Considering the current results of the "ACM & canon" thread poll, it looks like more people support them than don't. It didn't matter what they did,
something would alienate some of the fan-base. That's the nature of fandom, it's completely unavoidable. 'Aliens' alienated some of the fandom of 'Alien' (you're an example, too). 'Alien3' alienated some of the fandom of 'Aliens'. Colonial Marines is bound to not satisfy everyone, but it's not like they're retconning Alien3 out of existence. They're fixing an actual problem with the movie.