hotplug and recompiling the kernel have no influence one on each other. Stay calm: If you disable your...say...external CD, you can still recompile a kernel with "external CD support" without a problem.
The best for disabling hotplug is:
cd into /etc/rcX.d (X being the number resulting of running the command "runlevel" or "who -r" in the console)
rename the hotplug startup script (in RHat is kudzu):
# mv SXXkudzu sXXkudzu
now, the "init" program only looks for scripts beginning with "S", and not "s".
For your distro, the procedure is almost identical, but replacing "kudzu" with "hardrake", "hotplug" or whatever....