Are any of these souls paladins?
If not, then I don't see a problem.
The act is evil. Permanent, ultimate destruction of a person's essence for your own continued existence, whatever what the goals, no matter who's being destroyed, is evil, as I see it. Unless of course the person consents to it; if they do, then, hey. No big deal. Oblivion's not the worst thing to happen to you, especially if you're willing.
But, presuming these people aren't consenting, yes, sure. Evil act.
However...one evil act alone isn't enough to shift your alignment. Not as I see it. If these folk are paladins then, yes, that's bull. If not, though, then I don't see that one act, no matter how horrid, as outweighing all the other good things these souls apparently have done and will do.
It could definitely be the first step to evil, though. In fact, that might be a good way to run things. I'm not familiar with the product, but the souls might eventually get a feeling of pride and hubris over the thought that their worth is more then any one souls, and with pride comes the fall...
Edit: Wrong word, now fixed