If you wish to remove the submodules, you can do so with the commands
git rm --cached profiles/commerce_kickstart/libraries/jquery.bxslider
git rm --cached profiles/commerce_kickstart/libraries/jquery_expander
git rm --cached profiles/commerce_kickstart/libraries/jquery_ui_spinner
git rm --cached profiles/commerce_kickstart/libraries/selectnav.js
Once you've done this commit and push your code and you should be able to deploy once more.
If you still have problems, try this:
$ git rm -r ProjectName --cached $ git commit -m "clean up folders"