I'm a rather late to the party, but after reading through the thread, I wanted to jump in with my two cents.
This was my first exposure to Marla Mason, so I might be reading too much into the setting, but I'm inclined to come to her defense. The means in which Marla neutralized Malken were questionable, but but I think her reasons for doing so might have had some validity. Aside from his other flaws, Malken's first priority seemed to be convening all of the magicians to take power from Marla rather than to address the issue of the Fellport beast - that right there gives Marla a leg up on 'protecting the city' in my book.
Aside from that, I don't think it can be taken for granted that Marla would be able to prevent Malken from taking power. It's mentioned pretty early on that Granger, despite being inbred to the point of mild retardation, is guaranteed a permanent council seat and since Marla's dagger of office is an item of power, it's possible that things like Granger's seat are also assured by powerful magical means rather than pure politics. Given that, Malken might be able to unseat Marla fairly easily and then use his power however he wished. Given his priorities and that he all but promised to make Marla his concubine, I can't really blame her for wanting to prevent that from happening.
As for Marla taking out Malken in a magical duel, I don't think she could have. She talked about time magic being serious juju and (I believe) admitted that she wasn't able to do it herself, so it's possible that Malken may simply have been more powerful than Marla and her only option was to get the jump on him with something quick and dirty.
I don't believe that Malken was a racist, chauvinistic asshole because he was simply a product of his times. It's mentioned that his contemporaries thought he was rather terrible, both in accounts and as ghosts. Other people mentioned that Marla may have taken Malken out because of his potential to do harm to the modern population of the city and I think that's a valid position. I also think that it doesn't really matter that Marla was a woman, Malken seems the type to reclaim power in Fellport regardless of who's in charge and he just seized on Marla's sex as the easiest and most obvious (for him) justification to do so.
So no, what Marla did wasn't right, but it was (to my mind) reasonably justified.