Just to be absolutely clear here, no final decisions have been made about particular mods being allowed or not at this point. As with anything that is in development, everything is subject to change still
The point though is that we are making plans to deal with this and have started taking the initial steps towards implementing a solution. It is going to be a delicate balance and there will certainly be some grey areas and in these cases we will need to make a call one way or another, just as with any other design decision.
We definitely do not want to discourage mods though. Our ultimate goal is to make them far more accessible, while at the same time preventing abuses.