1. Couldn't you remove any Fortify Strength enchantments with a script in order to get base strength? Failing that, using Fortify Strength would be an unavoidable cheat, but hey, this method's not going to be perfect - plus if you check to make sure they're not wearing armour or weapons, Fortify Strength enchantments are less likely to crop up. You could even do a naked check in dialogue, too!
2. There aren't many useful 0 weight items. Keys are pretty much irrelevant, and gold (and any other obvious ones) can easily be detected with a script.
3. If someone is using a mod that changes the encumberance multiplier, they'd have to tweak a global in this mod before playing to set it right. Kind of like a "manual" compatibility patch.
Ok, it's not ideal, but it's something!