McNulty is not trying to impose his will on Stringer and Avon. His whole shtick is that he operates out of intellectual vanity. He can't accept that street thugs like Avon, Stringer or Marlo are smarter than him. That's also the reason he wants to after Stringer instead of Kintell Williamson, even though Kintell was dropping bodies and Stringer was not. He sees Stringer as smart, a worthy opponent, as opposed to Kintell who was a nobody. He's obsessed with arresting the big criminals not out of a sense of justice or because he empathizes with the victims of the drug trade, but because he wants to prove his superiority.
Even his problems with authority are just an extent of his intellectual vanity. Remember when the FBI guys profiled the "serial killer"?