If someone who is bound by the prime directive, knowingly does something that will greatly affect a civilisation, then the prime directive is breached.
The prime directive is also open to intepretation. If you look at TNG's "Two Short A Season", Mark Jameson supplied both sides in a war with the same amount of weapons, figuring that he had given both sides equal dominance. However, by knowingly supplying a less technologically advanced civilisation with starfleet weapons, he had in fact interfered with their society and caused a major change in the tactics of a war.
So you could argue that your commander used her interpretation of the prime directive to quickly end a conflict whilst saving her captain. In the long term saving many lives. However morally questionable this may be, it certainly gives you an idea of the kind of motivation a starfleet officer may use to justify a breach of the prime directive.