I think "Latent Image" is a fantastic episode, one of my all time favorite in Trek. No matter how annoyed I would get with Voyager's flaws, its episodes like "Latent Image" that remind me Voyager was still a really good series for the most part.
The mystery in the beginning, the ethical dilemma of the crew, the ethical dilemma of the doctor, it was fantastic. The concept of the Doctor suddenly becoming unable to function because he saved a friend instead of an acquaintance when they had an equal chance of living is a really wonderful concept - the kind of thing we didn't get in DS9 because it was so story-arc based. That's why I can appreciate Voyager as a sort of counterpoint to what DS9 was doing at the time, they both fulfilled certain needs - the need for big story arcs and drama, and the traditional concept episodes.
Only one thing bothered me and that was the lack of continuity regarding the timeline, since Kes would have been in sickbay, not Tom. A throwaway line explaining her whereabouts would have done it. Oh and its interesting how Seven has completely supplanted Kes in being the champion for the Doctor's rights. Here, Seven tries to convince Janeway that the EMH is more than just a hologram when it was Kes who had done it before in very similar circumstances.
Personally I had no problem with Janeway's reaction to the Doctor. She'd clearly been through the whole thing before and decided that the EMH really is a computer program that is essential to the ship and if it malfunctions, then of course it needs to be repaired.