While listening to this story the general lack of morals bothered me, for about two seconds. Then I asked myself this:
How do we impose our moral system on people with magical powers?
One could make the argument that with additional power comes additional responsibility. And it would be a valid argument.
But I don't want to go there.
Rather think of this: what is the mindset of a person with magical powers? How different is it from ours? Clearly a different set of rules applies here. And that set of rules is (I should think) imposed by the wizarding community. They must have some set of rules that they lay down to keep themselves in order. And it would surely be vastly different from our own.
I can't fathom what their rules would be, I can only speculate how I would draw up the rules. I wouldn't allow casual terrestrial law breaking (jaywalking, theft, mugging, rape, etc') because there is no conflict of interest. I would only allow murder under the most dire of circumstances. Think of James Bond, he has a license to kill, but doesn't shouldn't abuse that power. And when he does abuse it, it is revoked. The purpose of this license is to allow him to do his job: maintain world peace. (or those parts of the world that Britain has an interest in)
Similarly, wizards might have a license to kill or banish to the Dungeon Dimensions without having to get a court order. Because when you are dealing with this kind of thing there often isn't time for a court order.
They must, of course, employ a system of checks-and-balances to maintain order. When somebody does the wrong thing he or she needs to be corrected. Such a system exists in the world of the story, as evidenced by the institute for deranged and dangerous sorcerers.
Would the wizards choose a pencil-pushing, rule-following bureaucrat to lead them? I should hope not. Such a leader would have let several people die before managing to take care of the Beast. They need somebody who doesn't always play by the rules.
Do I agree with how Marla handled Malkin? I'm still not sure. But if I were there I would allow Marla the occasional, relatively harmless indiscretion. Without it, she couldn't do her job properly: protect the city. If she were constantly hobbled by what-ifs then she would be useless. A weapon in the hands of someone afraid to use it. Her greatest strength is her "Hulk smash" attitude. And it gets results. If we were to make her stop and rethink every decision, or drag her over the coals for actions taken, then she'd be less than useless. She'd be a liability. Because she'd still go ahead and do it anyway, only this time without support.
So, in conclusion, I don't think that we can judge her based on our rules or morals, and based on the conjectured rules of that universe, she was probably OK.