Not only is it comically villainous, it's the technical term for waste water from toilets. That is, sewage. Whoever is picking their names needs to be, uhm, shot.
Blackwater got it names from the swamps surrounding the area: "the Great Dismal Swamp, a vast swamp on the North Carolina/Virginia border, now mostly a National Wildlife Refuge...There, he created his state-of-the-art private training facility and his contracting company, Blackwater, which he named for the peat-colored water of the swamp.[10]"
But apparently if Blackwater wanted to shot the person that named it they can do that.
For trying to get away from the story book evil sounding-ness of an entity named "Blackwater", they sure didn't do very good with "Xe", which sounds even more mysterious and potentially evil-doing IMO.
Academi sounds a lot better though. And they do a lot US LE/gov't/etc. training which is probably what they would rather emphasize than their being a "private mercenary company".
For a long time, they did run a lot of training as their primary business, too. (US Training Centers, in NC, is one of the best firearms/combat training centers in the world. They also make excellent reactive target systems.)