Morale penalty is indeed fairly large. Something like 70% or 80% on the medium players. So moling does have its drawbacks.
Even if it didn't, I don't see how moling can be something that could be judged.
In TW2, you are meant to exploit every single resource to its full potential. In addition, moling isn't outrageously expensive. Sure, it's fairly expensive, but definitely far cheaper than some of the actions in game (ie. unlocking tribe perks, continuously shooting Gwen, etc)
I agree, moling does create an advantage in terms of resources and capacity. However, since TW2 allows it in its rules, I don't see what's wrong in it. In fact, I believe the "10% to upgrade a res building" is meant to be used for this purpose. If Inno finds it too powerful, it is their responsibility to restrict it, not players' responsibility to refrain from using it.
This is compounded by the fact that MOLing isn't THAT big of an advantage. An active farmer can more than make up for this advantage, and it gets evened out in later game. It's just a question of whether or not you are willing to spend the time.