Howard Butler has just uploaded Rtree 0.2.0. Once you've installed the spatial index library on which it depends (no longer distributed with Rtree, see the README), installation should be as simple as:
$ easy_install Rtree
Maybe we can work the dependency into the easy install down the road. I welcome ideas on how to do that.
Persistence of indexes, nearest neighbor lookup, and item deletion are now supported. See the doctests for usage examples.