Interesting, I never thought about doing it for security.
In that case, after all the chaos settles and the server is back up and stable, I would suggest trying modphp or something else for a day or two, and see if the problems still occur. If you don't have the same problems with it, there are two ways you can make it work.
1) You, could actually run separate virtual machines for each site, but that'd be a pain.
2) An easier way, would be to use a reverse proxy. Basically, you could start one apache instance for each of your sites, and have it listen on a different port. Each instance serves one site, which would keep them separate from each other, and thus give you the same level of security. Then, you run another instance of apache on port 80. It would use a reverse proxy to essentially forward requests to the correct apache process. Not the most elegant thing, but it would get you the added security while avoiding fcgid. If only apache had an option to handle each vhost in a separate process
