Well, the only skeletons I've ever excavated were on rescue digs, so if they hadn't been moved by us they would've been moved by a bulldozer. Some of those were Christian burials, and we were told they'd ultimately be reburied on consecrated ground. Probably they're still in boxes though, given the speed of post-excavation work... For burials (or remains) that pre-dated Christianity, there's not really much that could've be done to compensate, I suppose, unless the circumstances of any ritual surrounding their burial could be established. (Personally, I don't care what's done to me, and like Nathan says, the ones that are being dug up probably don't mind either.)