I think you did as you should.
I have found in the past that if I try to remove the MMA, the damage that is underneath provides a very poor foundation for the gel to stick to, and the nails are prone to lifting.
When the MMA is left there, and you do a rebalance instead, no lifting problems.
I currently have a client who is 'growing out' the MMA while I rebalance with gel, and you can see the difference between the two unfortunately.
BUT she is soooo enamoured with the clear glass look of the gel, she's telling everyone and PROUDLY showing them the difference, educating her friends. (I guess that's the bonus of sending nails out the door that aren't as nice as you'd like - the advertising). I prefer to paint over the nails, to hide the difference in colour. But she prefers them to be french and doesn't mind the difference. She says no one notices until she points it out. And she has re-educated a few friends and co-workers (unfortunately, none are in my area).
The gel shouldn't lift from the MMA, while the MMA itselt might lift with age. If it does... does as usual and correct whatever problems arise.
The other problem with removing MMA and exposing the damage to apply gels is the heat spikes and the sensitivity of the nails beneath due to the damage. Not all heat spikes are avoidable in some cases.
Best to avoid the discomfort. You can explain this to your clients.
hth's