I did this to see how much it would actually prune, but, as it pruned just over half of the CTxIndexs in blkindex.dat, I thought I'd pull request it. It only prunes up to the latest checkpoint as there is no undoing pruning, so chain reorgs cant undo transactions that have CTxIns that were pruned.
Note that the pruning process with -prune takes a lot of time with -prune (an order of magnitude greater than loading chain on my tmpfs-backed system) and eats around 400MB of memory to load the needed information into memory. -autoprune is much less resource-intensive, but the checkpoint has to exist before the given block is downloaded, so users upgrading will not be effected unless they use -prune once.
You can also run IBD with -autoprune to prune at each checkpoint.