Honestly, the solution probably would've been better the other way around, as with this setup, I see a good number of people just quit in frustration, while those who just want to play engie would find an alternate server to keep playing if it were the other way around, therefore filling both servers more reliably.
So after playing earlier, I saw quite a bit of frustration with certain teams with engies ruining maps for one team for two maps in a row. One was Turbine (yeah I know) - one team went normal classes, and one team was mostly engies with a few normal classes. One team naturally rolled the other, but even after entreaties from some on the other team, the engies still were as futile. It ended up in an rtv halfway through the map because the dynamic was so terrible.
The next map, Dustbowl, was surprisingly bad as well. Namely due to the engineers on offense not doing much and not caring either. The rest of the team decided it was nice to go predominantly spy & sniper for a while, although after the futility was exhibited people started to change classes slowly. Unequal teams probably made it worse as well. During that time I saw at least 6 people quit in frustration, with a few going to Red to try to start it up, although it never happened.
From what I can tell, it may not be completely the fault of there being a lack of an engie class limit, but it seems to exacerbate the dynamics quite a lot for those stuck with deadweight pubs trying to play engie or play terribly in general - in a normal situation, it might be easier to get a team scramble going with that, but the engie update may have obfuscated some perceptions of the dynamics. I'm not completely sure how to best solve this yet, perhaps I'll think up of something tomorrow.