Well you said it yourself, that the EMH was being a tool.
Frankly though I don't think the episode is saying that Seven was wrong to act out in anger. That reads into the events a bit much, and there's not supposed to be a silver lining to every pivotal detail. The whole point was that protocol was being followed earnestly in a situation with incomplete information, and it's contrived to the point where his own society overly deemed him guilty until proven innocent (if even). And go ahead and challenge me on this, but that is how sensational crowds, left or right, are known to treat things. It's arguable how much that applies to rape circumstances I must say, but to the point of this day and age where viral media influences administrative action, that's not really out of left field or anything.
I remember rewatching the episode when the review came about, and I think I remember, again, mostly tracking all of this to the EMH. I think maybe Janeway might have done something wrong, but the doctor is always considered the specialist in this episode. One of my posts here I believe talks about Tuvok, so I'll look at what I said about that.
It's a misguided episode for the worst, but I don't think the devil's necessarily in the details. I don't remember Janeway giving Seven a scolding look, and I don't think the EMH was trying to push shame on Seven.