Did you find yourself understanding why she might have done so?

Actually, it has a lot to do with what you said - she conflated Spike with Angel. She had to believe that a soul was a special, beautiful, difference-making thing because of Angel(us). Because of what had happened with that.

But even then, she never struck me as a bad person - but a fundamentally lost person - and someone in desperate need of a sabbatical.

Exactly. Buffy needed a break. Luckily, she has one now and I wish only the best for her in Rome.