You say Google Docs can’t handle the file size. Is this because of limitations of Google Doc or Paperpile (i.e. related to this issue here)?
If it’s a Paperpile issue we will make it our priority to fix this issue.
In any case, if you are using Word 2013 for Windows you might be able to be the first to use a Word plugin for Paperpile. It’s the only version of Word at the moment that supports the new API I mentioned above.