One of these again.
Firstly, it isn't unheard of for film DVDs to contain alternative endings. I Am Legend is one example.
Secondly, the problem is not that the ending was somehow undesirable. The problem was that it made no sense whatsoever. They are doing themselves a FAVOUR by rewriting it, because maybe now they won't be remembered as the people who managed to fuck up a brilliant story in the final cutscene.
That ending destroyed anything resembling a general theme across the series, and I'm just disappointed that they're not throwing it out completely and starting again.
On a side note, the value of art is in its interpretation, so honestly the artist's opinion is the least important opinion in the world.
(Former) Lead Moderator and (Eternal) VGC Detective 
