Hygiene is prevention, sub-cellular alteration would probably best be described as immunisation, and like all immunisation, there's no promise that the 'disease' being treated won't adapt to it.
Like antibiotics, there's no promise that anything we do will be permanent, biology changes constantly, which is another reason why we have to understand precisely what we are doing before we start fiddling on any large scale, the worst case scenario is that we put ourselves back at square one, or make some change that leaves us vulnerable in another way, or does some damage that doesn't even reveal itself until much later.
That's why we have to be careful, and we have to be sure.
Edit: It's a trap even a fair number of scientists fall into frequently, they assume that Man is the end product of evolution, and forget that our own bodies are evolving and mutating with each generation, as well as every organism around it.