Another aproach that may or may not work, depending on your exact requirements, is loading the keys into memory in blocks. If you're going through the indexes sequentially, then it may make sense to first load, say, 1000 from disk, then use those from memory. When you are done with that block, purge it and load the next 1000. This way, you spread your disk access out over time, with periods of pure memory access in between.

I suspect this might not work in your situation, but, as everyone else keeps saying, you haven't really provided enough information for us to know for sure. Hopefully by throwing random ideas out there, we'll come up with one that works. :-)