This sounds like a great idea. I would be fearful of it being based off of reputation directly, but I would encourage it to be something akin to applying for a job in Careers 2.0. Link a sampling of good questions, other relevant experience, etc. It could be done initially for Stack Overflow, and expended to the entire site if possible.
Furthermore, I think it would be more interesting if people were allowed to either donate to a general scholarship fund, or perhaps sponsor enough money to look at the applications and award scholarships, much as the Careers 2.0 site works.
In fact, why not just call it Scholarships 2.0?