My experience has been that this does not cause problems. You should be able to install anything that you choose with no problem, as far as I can tell all that it does is eliminate those annoying things that want to install when you hit some web-pages (like those clock weather enhancement things, as well as other spyware type crap).
I would also recommend that you get and install Zonealarm. A pretty cool personal firewall that will let you know if things are trying to phone home.
Uhm, please tell me what’s so bad about Gator? I use it for almost all of my internet passwords (excepting important sites, such as those which have my credit cards numbers or personal information).
Gator monitors the websites you visit, creating a personal profile about your apparent interests which it passes on, along with your e-mail address, to spammers looking for targeted demographics. Less subtley, it scans for keywords in web content, and causes pop-ups to appear, as though they are the sponsors of the web-pages you’re looking at. They also offer advertisers the opportunity to piggy-back on specific web-pages.
In short-- more junk and clutter!
Of course, that’s just what it’s designed to do-- it’s also crap software, and an added benefit of having it installed is that you’ll often find that your browser crashes spectacularly often-- sometimes even bringing down your entire OS, requiring a reboot. Great!