I assume people still eat meat in the Federation? Can't be all replicated junk. So if killing animals to eat meat is okay, why not killing of some extra-dimensional beings to ensure their survival?
There didn't appear to be any real intelligence in those creatures, maybe slightly higher than the average cow or goat that is consumed by humans back on earth. But still an animal of sorts.
Personally I think Janeway was too harsh on them and should have been a bit more understanding considering the Equinox crew was in such dire straits.
The way they were able to coordinate their attacks on Equinox and adapt their tactics is proof of intelligence. They were able to talk with them too once they had that alien guy with the summoner thing interpret for them. They sure targetted the fuel thing they were using the space slugs in with a vendetta too.
Was Ransom morally in the wrong? Yes.
Was Janeway's response out of porportion, hypocritical and down right insane at times? Yes.
First of all, it's not like she hadn't done some immoral things in her own command. Murdering Tuvix comes to mind for example. She decided all alone that she was going to kill one person against their will for the welare of two. Even the EMH thought that was unethical.
The alliance with the Borg is another example. She basically agreed to help the Borg kill their enemies in order to get home. I can't see how that's any more moral than using space slugs for biofuel.
Then her response to this. Sure, Ransom is morally in the wrong as I said. Janeway's response is to act as judge, jury and executioner all at once. Even when she captured his crew members she basically said, "I will kill you if you don't tell me how to find your captain so I can kill him for betraying the Federation's principles." Here's your hypocrite sign, Captain Janeway.
Even Chakotay, the freaking terrorist, had to restrain her little torture/execution thing. He had the right idea, instead of going off half cocked on some vengeful vendetta, try and make contact with the aliens. Oh and wait.. it even worked!
Ransom really wasn't a "bad guy" so to say more than a tragic character. It all started so innocently.. they didn't mean to kill the first one and it was already dead. Why not use it? Things were bad for that crew and it's easy to bend under pressure.
The fact that Ransom was trying so hard to justify this to himself, and could name the exact number that he had killed, meant he was remorseful on some level. You could argue one way or another if his crew deserves a death sentence, but I don't think Janeway alone should have been the one to decide that. Clearly her judgement isn't exactly sound in this episode.