I'd go with the Reverse Proxy route - it keeps all your separate domains separate and one run away mod_perl process dosen't affect the whole setup but only one server process.

Of course, you'll have to set up some monitoring scripts that check the logs of all instances to see whether all Apache processes are still running.

I have an experimental setup of Apache 2 as Reverse Proxy and several instances of Apache 1.3 as mod_perl servers behind it, listening to localhost:8xxx, and so far I haven't noticed any problems - but I haven't moved it into production yet.

For experimenting and later for the production setup, you can start your several Apache instances via httpd -C /path/to/httpd.site.conf, so that you'll only need one httpd binary for all sites. That setup won't work well with suEXEC, but as you can run the local Apache 1 servers as the respective users, that should be no great problem.