Ran across Mark Mayo's blog entry: FastCGI, SCGI, and Apache: Background and Future, which discusses exactly the things I've been struggling with this weekend. I have to agree that sticking an interpreter like Python directly into Apache is a lot of trouble. I've delved into Apache sourcecode, and the mass of macros and #ifdefs is enough to send you running away screaming. To try and graft Python onto that is just begging for trouble - and I've had some experience myself with grafting interpreters onto other things.
Running your webcode in separate processes just makes a lot of sense. You have much more freedom with choice of language and version of language. You can easily run things under different userids, chrooted, in jails/zones, on completely separate machines, completely separate OSes, maybe within virtual machines running different OSes on the same hardware.
Anyhow, thought I'd mention this because Mark's writeup made a lot of sense to me and I thought it was worth keeping a link to it.