That would be a delicate wire to walk on I think when trying to compensate and balance for both. Honestly, I think in the end, if you choose not to use the cheese, you are accepting a slightly greater difficulty to win a hard encounter. Which is fine with me, but I totally get what your saying about penalizing one group for the other. It would be really cool if they could achieve that perfect balance, but I think it might be more complicated to do so than we think it would be to make the fights totally even difficulty whether you want to use barrelmancy or not.
I think they could add menu options for "realism" (not exactly the word I am looking for) settings. For example, barrel cheese can still be done but you have to carry them with hands and hide from npcs that you are moving around their furniture, or smarter ones may attack. Food should have an option to heal or not. Animals climbing, well I can't think of anything to make that less stupid, but perhaps this one does not affect combat balance so much if you shift to humanoid form to climb a ladder then back to animal?
I doubt they will get perfect balance like you said, but if they do it around the more immersive playstyle then I would think more people would be happy because the stupid stuff would be there for everyone to use, and people who wouldn't think of ever using it would not be stuck with things being too difficult. I don't mind it being harder without the cheese, I like challenges, but perhaps there are a lot of others who do not like this and they should not have to do the things that make no sense just to progress.
