Perhaps without adding a high amount of useful information, I just want to voice support for this. While writing my thesis, I had to disable the babel package since there were incompatibilities with the thesis template I was using.
I feel that making this configurable on a per-document basis is definitely the right way to go. I also think Richard's suggestion "What would really be best is if we had a central place, in Document>Settings, where all such things could be set, for every package we automatically load. Maybe a combo box listing them, and then when you choose it, three radio buttons: Load Always, Load As Needed, Load Never. Right now, we have quite a few such settings scattered about in different places, for the math packages and other things. But users are always asking for finer control of package loading with almost every package we load." would provide a very nice solution. Just my two bits. Jacob