"I'm not sure why this HERV couldn't have simply gotten deleted from the orthologous position, somewhere between the human/chimp common ancestor and modern humans. What exactly is the problem?"
The integration site is intact.
However, let's say that it wasn't. As you point out, all musings in this area are hopelessly (but unfortunately necessarily) tainted with secondary hypotheses to explain details. The problem is that there is no way to test and verify a hypothesis, as there are any number of alternate, secondary hypothesis that could be invoked to save any other hypothesis.
And so, as I pointed out, this, just like anything else pointed to by evolutionists, is a potential falsification.
That might be troublesome, except for the complete lack of alternative hypotheses, plus a supporting infrastructure from other sciences.
As long as ID advocates behave like Scientologists and refuse to reveal the secret identity and methods of the Designer, evolution is the only game in town.
What does this mean? The virus is gone but the surrounding DNA is OK? So?
I pointed out no such thing.
There are scads of endogenous retroviruses. It would beggar belief that one had not been deleted somewhere in the human ancestral line.
You seem to think I'm a devoté of naive falsificationism. I'm not. A well-established theory like evolution could be falsified, but it would to take more than one apparently anomalous result. Haldane's bunny in the Cambrian (which, of course, was just a quip on his part, anyway) would be a serious issue, but it would likely give rise to a lot of speculation that it wasn't a bunny, or it wasn't in the Cambrian. What would kill evolution is if bunnies, and dogs, and chimps turned up in all sorts of palaeozoic strata. They haven't.