I'm a firm believer in the old saying, "If it's not broken, don't 'fix' it!", which is why *most* of my Joomla sites are still running PHP4.
Yes, you understood correctly about the glpbals.php tweak; it does attempt to mitigate register_globals=on. Whether or not it is more/less effective than actually setting them off is somewhat debatable - it *does* seem to plug the potential hole.
In reply to:
set register globals to off. If I did, would that effectively solve all the security risks (assuming all my components and module still function)?
I don't know that it is *ever* correct to say that *anything* "would ...effectively solve all the security risks", as anything accessable on the web risks being subjected to continual attacks. Think of it as an "arms race" - we plug an exploted bit of code, the bad guys find another attack vector, rinse, and repeat. Traditionally, the register_global=on setting has been popular with attackers, and changing it *does* eliminate that exposure, so it *is* a "good thing(tm)" 
The code you need to change in the script is to add a "substitution" regular expression, similar to the one used to modify the max upload - if you will be patient with me, I'll inspect the PHP4 php.ini file for what is needed, and post a code snippet later tonight for inclusion in the script.
There won't be any need for apache to be rebooted, as (I assume!) you *are* running PHP as CGI - all of this depends upon that. It *would* need to be rebooted if you were running mod-php as an apache module. When running PHP as CGI, the php.ini is read upon execution of the php.cgi, so apache doesn't care.
--rlparker