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Nope. The remove option just removes the symlinks for all runlevels to the apache2 init script. This way the service will not start again on boot.
You can take a look at the manpage for more details.
or you can chmod it like "sudo chmod 600 /etc/init.d/someunwantedscript" (without quotes, someunwantedscript = your stuff) that keeps the sym.links but not execute the script at startup. this is a easy way of temp. exclude it at startup. other debian way is to replace the letter S with a K in each run level (like S30gdm replaced with k30gdm in /etc/rc3.d disables the gnome display manager at startup
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