BioWare will continue to hem and haw about this situation for as long as possible, and I can't honestly blame them for wanting to. Really, there is no way for them to win in this situation; the "fan base" has them cornered when it comes to every option, with those being:
A) They leave the game as is, and claim that the original game is "as intended". The "Retake Mass Effect" movement will cry foul, and will ask the gaming community to both disown BioWare and to boycott any upcoming games. People will continue to send complaints to the FTC and BBB, and this controversy will continue.
B) They work pro bono to complete an entire new ending to the game. If it differs from the endings written by the fans, people will still be angered by the new ending; if it uses a plot point that a fan did come up with, people may enjoy the ending, but will persecute BioWare for being unable to come up with "original" writing anymore. Either way, Mass Effect 3 will permanently have that '*' next to its title in gamer history as being one that "could've been written better by fans".
C) They work (for pay) to complete an entire new ending to the game, and sell it as DLC. Gamers across the internet (regardless of whether they played the game or not) will declare this as clear and definitive proof that EvilArts has corrupted all that is/used to be the BioWare that everyone grew up with and cherished. See the consequences for option A, except replace the "fix the ending" banner motto with "split from EA". Yes, I understand that many have stated that they would be willing to pay for a fix, but you know that an argument like the one above will arise.
While I understand that they were the ones that dug this hole by making the ending how it currently plays, it is the fans that are covering said hole, thereby eliminating any chance of escape.