Hi Joe,
I would suggest that after the teachers copy the homepage template into their course that they click on the HTML editor and copy all the code, then create a new "production" homepage and paste the code into that.
This would solve the problem of them accidentally overwriting their homepage when you update the template and it gives them the ability to update the template and see what's new. From there they can determine if it is something they want to copy the code again and make a new "production" homepage from it.
I know this is not ideal but I think that is as functional as it gets with the given feature set and functionality of Commons updates.
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