Although the whole thing is, of course, nothing more than a hypothetical, the obvious answer is: of course Super Mutants would be immune to HIV.
The way FEV works, if I'm not mistaken, is by essentially correcting or destroying anything that doesn't conform exactly to the infected organism's natural DNA sequence (including sperm/eggs, hence the sterility issue). So it doesn't matter what way HIV goes about it... if it infects a cell, the DNA is altered, and so FEV would destroy or correct the abnormality. I don't recall how the "side-effects" that make a Super Mutant a Super Mutant are supposed to result from it... I'll have to refresh my knowledge on that.
As for the topic... while it is, of course, a great leap forward having a map of the cold virus's bits, it'll probably be a quite a while before anything comes of it. First they have to actually find these similarities between all the different strains, then they have to find a drug that affects that specific thing, then they have to do endless trials to make sure that drug isn't doing more harm than the virus itself (and considering it is only a cold virus, I don't think most people would be willing to trade, for example, impotence and a runny bowel for a sore throat and a runny nose), etc. and so on.