I watched the deleted scenes and I certainly agree that Halloween and Goodbye Love should have been left in, although I don't think the alternate ending should have been used.
On the commentary they talk about the alternate ending, and they explain why it wasn't used. They wanted to make people realise that Angel really was gone. It would have seemed like "Oh, it's okay, he's okay, he's back" if they'd used that ending, and it would have destroyed the reality that is RENT.
Although it was beautifully filmed, I just don't think that ending should have been used. RENT is supposed to be an account of real life, of the hardships faced, the relationships made and lost, and the realities of every-day life. If they had brought back Angel, a person tragically lost to AIDS, it would have made AIDS seem like a trivial thing, which it isn't. I think it was more moving to just have Angel in Mark's film, because it was a memorial to his life, and the mark he left on his friends.