I have done similar changes to Satchmo internals in the following way:
It should be possible to copy the relevant file from the Satchmo installation into your django application. If you set up your Satchmo shop according to this recommendation, that would likely mean copying satchmo/apps/satchmo_store/accounts/mail.py to /localsite/accounts/mail.py. The idea is to automatically load the local copy instead of the original.
In your local copy of mail.py you could then replace the send_store_email() function. Keep a note so that you will remember your changes when it comes to a Satchmo upgrade. Quite likely the original file will still be the same, and your override will work even with future versions.
In other cases when you have to change some class behaviour you can also subclass the original class with one changing only the relevant methods, while keeping the original name.