The automatic co-termination has pros and cons indeed, this is one of them. I know Meraki are working on this but I don't know what the status of that is.
At renewal I'd just fetch an export from the inventory and create a pivot table based on the "Network" column in the inventory. That way you know exactly what number of devices is in which site (Network) and split up the renewal invoice that way.
The only issue with this is on the initial purchase of new equipment and their licenses:
Imagine site A bought 3 camera's with 3 year licenses, and 2 years later site B buys 1 camera with a 3 year license. Due to automatic co-termination, for site B the renewal would actually come earlier than the 3 years they purchased, because part of the value of their license will be "transferred" over to the site A camera's. That's the nature of the co-termination, but it's not fair to the site B guys.
The mathematical system of the automatic co-termination is pretty transparent though, so I guess you (or the bookies, they love this stuff) could work out the maths yourself to discount them for the first renewal.