Why does that seem to be a bad idea? I agree it is not so nice that you can't just yum update those packages anymore, but according to
How do I enable Piped Logs for Apache Web Server: "If you have more that 900 domains, you still have to recompile Apache and some other system packages as described in article
260". If it's the only solution, I don't think it's a bad idea. Or you'll have to get more servers.