I've heard this meta key is obsolete, but they are still getting created every time a user registers. Can I prevent this? I'm trying to slim down that table.
User levels are deprecated, not obsolete. Deprecated features should still be expected to work but should not be used in new code. The point of deprecation is to provide code authors time to update software and thus avoid breakages when the deprecated feature are finally removed.
Leave this alone.
Besides which, it is a very insignificant "problem" you are trying to solve. MySQL can handle a lot of data in a table.
Emerson, I'm running into the same sort of issue with the network I work on and the wp_usermeta table has seemed to be the main cause.
I'd love to compare notes with you on what can be done about it. If you're interested contact me on twitter first, username pap3rtig3rs