The Season 1 episode "Angel" was on TV the other night, and I noticed something I hadn't before: the plot, such as it is, mirrors what we just saw in the comics. Angel has been hiding his true identity from Buffy, helping her from behind the scenes while at the same time manipulating her, and goading her into attacking him despite his own desire to be with her.
When it finally comes to a confrontation, he does explain himself, but the kicker is that it's not that much of an explanation. Buffy has never even heard of a vampire with a soul. What's so convincing about Angel saying that's what he is? It clears up the gap in his murderous rampage, but any handy lie could have done that. He kills Darla before Buffy's eyes, but by that point she already believed him and had put herself at his mercy.
Looks like she just went ahead and took his word for it. He had been good to her before he was revealed, and she felt a connection to him after it. Stupid? Immature? You decide, but there are two crucial things to notice here. First, her gut was right the first time, as Angel did indeed turn out to be a good guy. Second, SEASON ONE. This is how Buffy's character, and her relationship with Angel, was set up from the beginning. It's all or nothing, and she chose all.
Put the same story on a much bigger scale. Angel's deceptions turn into vast conspiracies, but he's still Angel. Buffy is seeking revenge for 206 dead Slayers instead of her wounded mother, but she's still Buffy. The two of them have shared a decade of love and agony instead of a few flirtations, but they're still battling the same demons.
Of course Buffy is going to make the same choice.