How do you propose this work? Like a bulk edit checkbox next to the listing of email templates with an action to set a particular from email on all selected to one specified?

I would suggest that the Department and From Email both be part of the Signature. That way, when you select a signature, the From Department/From Email and Email Signature are all automatically set. If you leave the signature blank, you can fill in what you'd like for that specific email. If you need something different, simply add a new signature..
This is critical for a new setup - it takes several hours to modifty the From Department/Email on every template.