It seems you think paternalism is okay if it is pure in intent and flawless in execution.

You're twisting my words. I said that FAI paternalism would be different - which it would be, qualitatively and quantitatively. "Pure in intent and flawless in execution" are very fuzzy words, prone to being interpreted differently by different people, and only a very specific set of interpretations of those words would describe FAI.

It has been shown that vulnerability to smoking addiction is due to a certain gene. Suppose we could create a virus that would silently spread through the human population and fix this gene in everyone, willing or not. Suppose our intent is pure, and we know that this virus would operate flawlessly, only affecting this gene and having no other effects.

Would you be in favor of releasing this virus?

I'm with Alicorn on this one: If it can be made into a contagious virus, it can almost certainly be made into a non-contagious one, and that would be the ethical thing to do. However, if it can't be made into a non-contagious virus, I would personally not release it, and I'm going to refrain from predicting what a FAI would do in that case; part of the point of building a FAI is to be able to give those kinds of decisions to a mind that's able to make unbiased (or much less biased, if you prefer; there's a lot of room for improvement in any case) decisions that affect groups of people too large for humans to effectively model.