If you run FileProtect and then switch back to DSO, DSO works similar to having FileProtect disabled since PHP processes run as the user nobody. There shouldn't be an impact, but you can re-enable FileProtect using /scripts/enablefileprotect and then running the commands I noted to backup Apache configuration and so on afterward:
As for upgrading Apache, if you run EasyApache, the option is in the Exhaustive Options list and can be de-selected there as well:
cp /usr/usr/local/apache/conf/httpd.conf /usr/local/apache/conf/httpd.conf.bak110531
Any settings on an EasyApache compile will carry over to the next recompile provided you select to use the last saved settings.
Fileprotect (Prevent Users from reading other webroots)