I'll definitely be keeping an open mind during the rewatch. Already, Janeway is rising in my estimation and I even have an example of her attitude being readjusted by Kes in "Eye of the Needle" when she insists that the Doctor is just a hologram and not a living being.
Which won't be the last time that Janeway is forced to question her prejudices concerning the Doctor and readjust her thinking.
True. She and THE REST OF THE CREW tried to save him from a guilt feedback loop that threatened to disable his program by erasing certain problematic memories. In this case, she once again listened to criticism, this time from Seven, and decided to try another solution. In fact, she personally assisted him as he tried to work through the problem ("Latent Image").
She also treated him like a real person, probably more often. She lets him be "sent" to earth in order to help his creator, Dr. Zimmerman, recover from what was thought to be a fatal illness, even though there was a chance he wouldn't be able to return ("Lifeline"). She was almost too easy on him when he betrayed them to the photonic rebels in "Flesh and Blood" because she felt equally responsible for having provided the Hirogen with a holographic technology. And, she was willing to let him stay behind "for love" in "Virtuoso." To me, these are very significant actions on her part and shouldn't be overlooked.
It's easy to fall into a negative Janeway attitude if you pick and choose certain episodes and fail to look at the entire series. Ignoring the positive things she does is really unfair to the character. In the case of the EMH, in the long run, Janeway eventually treats him the same as she does her "flesh and blood" crew, even passionately defending his rights as a writer in "Author, Author."