Right. So there could in principle be something to this. Even if this fly-sperm theory turned out to be real, though, I wouldn't be surprised if it turned out that nothing like it happened in mammals, for some basic biological reason about which I know nothing. And as I said, the evidence provided by this one study is pretty slight. 'Studies have shown' is mostly unscientific nonsense; most studies don't really 'show' anything at all. It takes a lot more work than just one study to pin something down.
The general idea that genetic material can get transferred by other channels than parent-to-child has been a warm one for a while, I believe. In fact we know it happens all the time: viruses exist, and they are just like computer viruses — because computer viruses were named after the biological ones. ('Virus' is Latin for 'poison', and it used to be a generic term for any kind of bad biological stuff that caused illness. Once the germ theory of disease was accepted, it was noted that some infectious agents seemed to be able to pass through filters whose holes were small enough to catch most other germs. Whatever those things were, they were classed as 'filtrable viruses'. The reason they're so small, and yet dangerous, turned out to be that they lack all the usual reproductive infrastructure of a living cell, and simply act as genetic parasites.)
An even more interesting aspect of telegony, it seems to me, is non-genetic heredity. If you just throw DNA in a jar, nothing living crawls out. You need a mother to produce a child, and all the complex biological conditions of the mother's body are bound to have some consequences for the offspring — not just her DNA. While the point of life (in some sense) is to propagate DNA, basic cause-and-effect means that there is a parallel track of biological influence, beside DNA, running through all of biology in general. DNA is the core, but the husk is there, too. Identical twins have identical DNA, for example, but they don't have identical fingerprints, let alone identical brains.
Focusing mostly on DNA is certainly not stupid at this point, since DNA clearly has an enormous influence on everything about an organism. But to some extent, focusing on DNA is like looking for your car keys under the lamp post. We know how to look at DNA much better than we know how to look at anything else. DNA is so important, and so much easier than other things to investigate, that it makes sense to put almost all of our research investment into DNA, right now. That doesn't really mean that DNA is the whole of the story.