As you point out, the episode hands Harry Kim exactly what the character wants (to be on Earth with his fiance), and the character doesn't struggle for a single second whether or not to leave. If that's not incompetence, then in the very least, it's not very dramatic.
So, you agree that Harry has no problem deciding to return nor does he really have a problem returning (thanks to Cosimo,) and you agree that this isn't very dramatic. Why do you then persist in assuming that the story is really about Harry? Because the episode didn't follow convention in showing us the hero in the first shot? The one who had a real problem was Tom, the one who had to make a tough decision was Tom, the one who got the high points, dramatically speaking (story beats I think they call them,) was Tom.
Admittedly it is unusual, if not downright daring, to bring on the true protagonist later in the episode. But it is a legitimate dramatic choice. I think that you have to simply assume Voyager is terrible writing, in defiance of what is actually on screen, for whatever reason you really have, to defend the case.
If Non Sequitur has a problem, it's Tom wasn't acted forcefully enough.