Looking forward to experimenting with the new version, with whatever slider set to "loads of extra new units".
A totally different approach (and this is just purely hypothetical) might be that you don't actually build new units in the RTS part.
The RTS part would consist of deploying your units and capturing building sites which can be used to build defensive structures (turrets) and repair/healing facilities, as well as buildings that provide a boost to your units.
Each unit on the map gets you a squad in the RTS part and recruits can be used to replace units in a squad - if the entire squad is gone then you lose that unit completely. The supply cap could either be removed or apply to defensive buildings instead.
Potential problem there: If you screw up an attack, without getting new units, you can't recover from it.
And further, if you don't bring certain units to the battle (say shamans), you can't use them and will have to rely on immobile structures to fill in the gaps (like healing).
I think that not being able to build new units in RTS mode would be too crippling to the gameplay to be worth adding, for the downsides you pointed out.
