Penalties would be more interesting if you had the option to opt out of the ideology system. Since that isn't present, I would rather avoid them directly.
Maybe if each tree had an plus/minus tied to the number of tenets you had adopted? ie,
Freedom: -2% building maintenance costs, +2% unit upkeep (both per tenet adopted)
Order: +2 hammers in every city, city state influence decays 1% faster (both per tenet adopted)
Autocracy: -2% ideological unhappiness, -0.5% science (both per tenet adopted)
These are about as well balanced as a breakfast of marshmallows, I'm sure, but I think it's a reasonable way to go about the issue that helps further specialize your civ away from the non-preferred VC for the ideology.