Here is a small patch to allow zip file uploads (just one file per zip). See Issue 280 http://bitbucket.org/galaxy/galaxy-central/issue/280/allow-zip-file-uploads
I'm new to Galaxy and Python, so I hope I didn't break up anything in the process :-) Find attached a diff file, which I created by executing:
hg diff tools/data_source/upload.py > upload.py.diff
Please let me know if you prefer another format. Yours P.