About two months ago one of my coworkers added his virtual environments into our Git repo and pushed it.
I removed it in a subsequent commit/push and added it to the .gitignore.
However, since then we've had about 500 more commits.
Is there a way I can just remove his original 90k line commit altogether from Github and our local repos without causing any issues?
You could create a branch from the commit before the problem, and a branch on the first commit after the problem. Then rebase the second onto the first. Then, if you reset your master to point to the new tip of that branch, and delete all refs to the other line, GC will eventually destroy the items.
Of course, you'll probably want to re-clone everyone's repo afterwards, since this is such an invasive change that involves updating a lot of refs (assuming from your description that a lot of things have happened on the repo since this).
Github has a help page on removing sensitive data that would apply to your situation also (there are only a few Github-specific parts which you can ignore).
The good news is you can remove the old commit.
The bad news is that you may cause trouble with your collaborators, unless you can communicate very effectively that the entire history of the repository will be changing. They will need to rebase all their working branches against the new history.
