TNG's PD has always struck me as condescending and paternalistic and have no patience for it. Why should the folks on Tyree's world have kept fighting so, when they had a history of relations before the guns came along. Why wouldn't they have one day just made peace like any rational people. Instead, the story treats them as children who can't handle their own natures or relationships between communities because of these 'superior' cultures' interference.
If the PD is so important, in Voyager, the Caretaker was an outside force himself, and possessed a technologically more advanced than the Federation. Why shouldn't they prevent more advanced Caretaker tech falling into Kazon hands? They certainly wouldn't allow the less advanced tech of the Federation fall into Kazon hands.
Once he died, Janeway was left in possession by default, more or less, not only by being there but was brought there by the Caretaker. Being in possession of superior technology she'd be remiss in PD responsibilities to let advanced technology in her possession to fall into less advanced people's hands. Her destroying the array would seem a justifiable following of the PD as I see it.