. . . then I really don't have the option to use mod_perl.

In the case you setup, that is true. I'm not sure what your point is, though. If you can't use mod_perl, then you can't use it, so you don't even need to ask.

Are there any other reasons that you might choose one exclusively over the other?

IMHO, mod_cgi should only be used for legacy code. mod_perl might need a little more discipline to use correctly, but the advantages are well worth it. Not just for speed, but for extra flexibility.