clean up .pyc files in virtualenv stored in souce repository after the fact?
That is fine, just remove them! 
Python auto-generates them from the corresponding .py file any time it wants to, so you needn't worry about simply deleting them all from your repository.
A couple of related tips - if you don't want them generated at all on your local dev machine, set the environment variable PYTHONDONTWRITEBYTECODE=1.  Python 3.2 fixed the annoyance of source folders cluttered with .pyc files with a new __pycache__ subfolder
I've created a virtualenv for my project and checked it into source control.   I've installed a few projects into the virtualenv with pip: django, south, and pymysql.  After the fact I realized that I had not set up source control for ignoring .pyc files.    Could there be any subtle problems in simply removing all .pyc files from my project's repository and then putting in place the appropriate file ignore rules?   Or is removing a .pyc file always a safe thing to do?