It's also the title of a very good science fiction novel that I would say treats the word without negative connotations.
Though this only really works if you're doing something orthogonal to the original word and build enough of a brand to make it stick.
I would HOPE that people would learn from it, and end up with a slightly better vocabulary, and be thankful for it.
On the flipside, it's NOT a commonly used word, so SEO for it (at least for the name) should be drop dead easy. A search for Diaspora should contain either a wiki link to a disambiguation page, or an article about them. That's about as good as you can hope for, SEO wise, though I obviously have to concede that the name fails the obvious pronounceability test, but as more and more of our interactions are relegated to clicks, that's becoming less of an issue than it used to be.
All that said, I'm still rooting for their core mission. Social networking deserves to be an open protocol, not a closed service.