why did the cleaner shoot the black woman?

Because in the 1990s black lives didn't matter :) Just kidding. hehehe

Anyway, YES, he killed her because she was freaking out. You have to keep in mind that killing is a lot of what this organization is about. More importantly, it's a secret organization therefore you can't afford to have someone freak out on missions like that. You need to stay focused, do what you need to do and get out clean. That's why they have a cleaner, for when things get messy.

If you're unable to complete missions and further compromise other agents in this case Maggie/Nina then you are a liability to the organization so they are safer getting rid of you.

And yes, it's harsh but I think it looks this way because you get to see this lady for a little bit. She seems really nice, funny, friendly and she's helping our main girl. But she's like every other recruit we see for a second on two in training including Nina/Maggie who was also at risk of being killed if she didn't shape up.

This movie *beep* stunk the original is much better bridget fonda was a joke.

She was way too naive and got cleaned because she was a dirty snitch.

She was stupid to call it in, though the security guard Victor shot could have screwed things up. Maggie knew calling it in was a death sentence.