That's not necessarily true. The removal of a mutagen may not reverse the mutation (of course there is always the possiblity). Often in genetics, once a mutation has been established, there is no going back. As per our early point. I would assume that the lifespan has been greatly depleted by the mutation (although we never see any females or offspring, hmmm....) and thus the mutations have been firmly established within the breeding stock. Even if we had some clean genetics to introduce, we may never be able to completely remove the mutations.
Depending on the properties of the "shrooms" (as you call them), it is quite possible that, if they have an intellect depleting affect and instill both aggression, lack of judgement and blindness, then the affects may be somewhat alleviated by the removal.
I would, however, suspect that, since the dissappearance of the Dwemer, that the "shrooms" have not been a full part of their diet (why would they use them?).
The Falmor have never struck me as particularly unintelligent during my encounters with them (after all, they have mastered a good deal of magic and are quite good strategists and have built a relationship with the chaurus and spiders - although I'm not sure what it is - it could be symbiotic or synergistic). I suspect that it is their environment that has retarded their development to it's fullest extent rather than a lack of ability.