The very awesome Minor League Splits website now has defensive numbers -- specifically, Total Zone figures -- for minor leaguers dating back to 2005.
Total Zone is a system created by the guy behind CHONE, that is sort of a variation of ZR.
This is, as far as I know, the only higher-level defensive data available for minor leaguers. Obviously, it isn't perfect (any more than any other defensive stat is), but I think this is a good start.