This puts me in mind of the "crowdfunding" model that was applied, successfully I think, by Kristina Kilgrove at Vanderbilt for a Roman cemetery DNA study. I don't think she had enough funding to do Y-DNA, though.http://lightyears.blogs.cnn.com/2011/11/11/who-were-the-99-of-ancient-rome/
One of the problems is that the people analyzing ancient Y-DNA factor in the cost of their multi-million dollar lab, and million dollar sequencer, charge $10,000 or so to insure that the sample isn't contaminated, and then
run the $29 test for one SNP, or whatever.
I have to think there might be a more quick-and-dirty approach. I recognize that dirty is a dirty word; but these bones have
been underground for a few thousand years. And they do stuff somewhat akin to washing them in Clorox and baking them.