I spent some time with Apple today on this problem and think that there is a solution to at least get sharepoint working with safari again.
Before starting, two comments:
(1) You will have to reinstal some pluggins like flash after this.
(2) You need to read the instructions completely. If you don't and just delete everything from the /Library/Internet Plug-Ins/ folder, you may have to reinsall OSX!!!!
I had to perform this in safe mode. You may not have to do this, but if you can log in to the site from safe mode, you might conclude that this is a good option.
Now, what I did was follow the manual uninstall instructions in the following article.
http://support.apple.com/kb/TS3230
In addition I deleted everything from the following folders if they appear in either ~/Library/ or /Library/
LaunchAgents
LaunchDaemons
startupitems
I suspect that I will see the issue again after I install one of the pluggins again, but now I can fix it, or maybe diagnose exactly what the problem is.