The Dark One mindtrapped her as a punishment. If this is her last chance to serve him, having to work at Moridins' direction at all times would undermine her full range of options to accomplish anything.

And Moghedien tried to balefire Nynaeve even though she was not ordered to do so, so Moridin was not aware that she made the attempt, implying that he is limited in his control over them.

He may hold their mindtraps, but aside from the ability to harm their souls, it doesn't look like any Compulsion is forcing them to do exactly what he says.