You said you were trying to update via http://download.eclipse.org/releases/helios/
, so sounds like you're still running Eclipse 3.6 (Helios).
According to the EGit FAQ, the latest version of EGit that is supported on Helios is 2.1.0.201209190230-r. It also says:
If possible we will not prevent usage in older releases but if we want to take advantage of new functionality only available in one of the latest two Eclipse releases but not in older releases we will update dependencies which will in fact discontinue support for older releases.
You might have bumped into one of those dependencies that break EGit on your version of Eclipse.
I recommend either:
Install EGit 2.1, the last supported version for Helios. Under "Help->Install New Software", add this site: http://download.eclipse.org/egit/updates-2.1/ . Install EGit from there.
Upgrade to Eclipse 3.7 (Indigo) or 4.2 (Juno, the latest) and try again with EGit 2.3. Be warned that upgrading Eclipse might open you up to new problems.