Can I prevent “wp_user_level” from getting added to wp_usermeta on registration?

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.