That's why another of Janeway's mistakes was to put up with the EMH's whining in "Latent Image". She should have told him simply that he was the only doctor on board, and they couldn't afford having him decompile himself. So the erased memory was staying erased, period, exclamation point. Put on your holographic big boy pants and DEAL WITH IT.
I think a good part of Janeway's mistake is pussy-footing for half the episode to begin with. Yes, I agree that there's a line where she has to say that the decision was made and he just has to live with it. But that requires an element of "Trust me, Doctor."
In "Clues, if Picard had asked Data, "Are you hiding information from me because doing so protects this ship and crew from harm?"
"Yes, sir."
"Lethal harm?"
"Yes, sir."
At this point, Picard is faced with a choice: go back, or trust Data. There's a decent chance he simply trusts Data and that's the end of it.
Janeway spends half of the episode, "What? Doctor, what? What are you talking about?" She didn't sit him down right away and tell him what she could. There was an incident. There was an incident that created a moral conundrum that your program could never have anticipated. The medical issue that you were faced with was resolved, but your program still couldn't resolve the issue.
This ship needs a doctor. You're it. To resolve the problem, I had the incident wiped from your memory, and it's going to stay that way because this ship needs a doctor. As that doctor, you have a responsibility to this crew, so I'm asking you as their doctor to trust me. We almost lost you to this once and we can't afford to take that chance again. Voyager can't afford to lose you as a doctor and we don't want to lose you as a friend.
Ask for trust. If he pushes it, then Janeway can hard line how ever she has to, but all she's doing is already agitating him and making him question his sanity.