Another controversial opinion, though I'm still happy to keep discussing "Oops" children like Jack and Ziyal, and probably David...
Captain Janeway's initial actions in "Latent Image" were right. Voyager had only one medical doctor available, and the memories threatened to destroy him. In light of that, Janeway should have quietly and firmly told him that she would allow him to remain aware of her actions, but that he would not be allowed to access the memory of the incident itself. Just as she told B'Elanna that Voyager needed her, so she was just going to have to take Crell Moset's treatment and deal with it.
If he still wanted to restore the memory a year later, that would have been another matter. At that point, they were in regular contact with Starfleet, and if the Doctor wound up decompiled, Zimmerman could send another EMH. At that point, while losing the Doc would still have been tragic, it would not have put the whole ship at risk.