Like the OP, I wasn't sure I was going to like this episode, but I ended up changing my mind. I liked both the A and B stories, although I do have to admit that I was skeptical about B'Elanna being the one to make the alterations to the Doctor's 'Family Life' holo-program.
This didn't occur to me when I watched it, but reading your sum-up. Notice how the kids the son falls in with are Klingon, and he wants to embrace Klingon warrior culture. If the Doctor wasn't going through such a harrowing ordeal that's some Freudian programming by B'elanna right there.