About Prey and Janeway and Seven attitudes, I'd say that both played their parts, with equal rights and wrongs. That resulted with Janeway privileging a humanitarian gesture toward a wounded sentient being, regardless the dangerosity of its nature (it would be interesting to see until what point Janeway would be ready to put her crew's safety on hold to save an unknown creature, wounded or in need - her "guests" have not all friendly intentions! <grin> ) and Seven, acting to protect at all costs her new Collective, even if this implies that she re-adopts her reflexes of former Borg: implacability & efficiency.
About the comparison between Janeway and Ransom in Equinox (fs4's final & S5's ouverture), I would be more measured, even if I would tend to agree with Ransom at the end, when he said that it was easy to cling to principles when the Voyager's captain stands on a vessel with its bulkheads intact, manned by a crew that's not starving/dying. In fact, I'd say that Janeway's attitude & speech to Ransom & his remaining crew are particularly hypocritical in this episode : while she holds a strong moralizing discourse, mixing the protocol & principles to Ransom, she seems to forget that herself, toyed & broke the rules more than one time with the same protocol and principles, when she wanted to reach her goals at all coast.
-> in what, Ransom's decision to use the sentient beings as fuel, in Equinox (s4/s5, is different in the spirit from Janeway's decision to help Borgs to acquire a biological weapon they could use against Species 8472, biological weapon which wll be used afterwards to commit genocides against innoncent populations in all corners of the DQ as we will learn in Hope and Fear (s4e26). That she accepts or to recognize it, she armed Borgs arms, in their ambition to add other racess to Borg perfection, in full knowledge of risk (Chakotay warned her, even if I still think he had other motivations in mind, like his rather thoughtless detestation of Borgs!). And how has she come to that decision to choosing between the plague (the Borgs) and cholera (Species 8472)? Because her vessel & her crew were in danger if the crew had to meet & fight these both highly dangerousennemies. So, she accepted to make a covenant with the devil.
As for her attitude/harsh sanctions towards the remaining Equinox crew (she could have just give them a formal blame in their personal files & 1 month or 2 to do menial tasks, like to clean the ducts, etc...under close supervision before integrating the crew in using them in their field of competence), I'd talk about blind justice driven by anger and frustration of not being able to judge and punish the principal responsibles. I would have hoped seeing Janeway being as comprehensive/forgivable with them in following seasons as she was with the members of her senior staff! -> some good scripts and even an ard could have been written about Marla Gilmore and Noah Lessing's long and hard road to absolution... (I'm happy to see that some fanfictions refered to Janeway/Lessing's tense relationship to a mutual understanding at the end, to the point that he will be here to defend her when she will be question on Equinox dramatic events)
-> again, a captain gives orders and subordinates have to obey them, from the XO to the cadet from low decks. their opinions are not needed or required, regardless the people are on Earth or on a vessel. Period.