I'm probably one of the first to call Xander out over his hypocritical actions in the series, but this example isn't one of those actions.
As much as I hate to admit it, I do understand why Xander wanted Angelus to die. Angelus was choosing to end the world out of spite, for no other reason than because he wanted to. On top of that, he was Angelus, the worst vampire ever to exist, and that person wasn't just going to go away if Willow's spell worked. Yes, Angel would return, but Angelus was always going to be there, under the surface, and could come back at any time - in fact, he did. By deciding not to tell Buffy about Willow's spell, Xander thought he was doing the right thing, keeping the world a little safer.
Willow, on the other hand, is a completely different situation.
I'm no Willow fan, but even I can see that Willow was consumed by grief when she decided to end the world, grief over losing the love of her life, the one person she trusted more than anyone. Not only that, she was weighed down by what Giles did to her, and all the pain and grief of every person in the world was thrust unto her as well as her own. Willow wanted to end their suffering, put them - and herself - out of their misery because she couldn't deal with her own pain. Once she face her pain and grief and guilt, she became herself again, the person who had no intention of ending the world and wasn't in danger of doing it again.
Xander knew Willow better than anyone and he could see that she was lost in her own pain and that was the only reason she was on this crazy quest, and he knew that if he could get through to her, he could save not only the world, but Willow herself.
Angelus was a completely different story. Xander hated him, had no ties to him and Angelus was nothing more than a monster who did deserve to die, despite all the good that Angel had done up until that point and all the good he still had to do.
Xander is a hypocritical douche, looking down on Buffy for dating vampires while he himself dates and almost marries an ex-vengeance demon who has killed thousands more people than Spike and Angel put together. But in this instance, he was right to want to save Willow.