We weren't able to find any silver bullets. We used an orm to split applications for non enterprise clients. And then just installed a duplicate application+db in the cloud for enterprise clients and made sure to charge them for it.(30k+ annual subscription fee)

So to upgrade the application we'd upgrade the everyone application and then do the same with each enterprise client. We only had a few.

I'd recommend trying to avoid it if you can, and if you can't charging the appropriate amount of money which is an arm and a leg.