I don't see the Malon as villains at all. Granted, Voyager didn't get off on the right foot with them, but I think that Emck and Vrelk were just bad apples who weren't examples of typical members of their species.
In Juggernaut, Vesek and Pelk were much more sympathetic characters and the episode fleshed them out, so that they weren't one-note characters that Emck and Vrelk were.
I especially liked the interactions between Vesek and B'Elanna during this episode, where she changes her opinion of Vesek, if not his species, by the end of the episode. One can't blame B'Elanna at the beginning of the episode for her rudeness to Vesek, after having to deal with Emck and Vrelk, but Vesek showed her that all Malon aren't alike.
I never understood why they didn't have her tell him about the waste recycling solution that was rejected by Emck, as I think that Vesek would have surely been more receptive to it.
However, I fixed that in the fan fiction story I wrote about this very thing.
