I'm going with the philosophy that the PD applies only to pre-warp civilizations that are not supposed to know the Federation even exists, and whatever atrocities they get up to are their own business since they need to evolve in their own ways.
But the Federation is based on the philosophy that liberal humanism is better than other social and political forms. otherwise how can they rationalize things like wrangling with Klingons for control of a planet or ignoring the Dominion's insistence that they stay out of the Gamma Quadrant? The Federation's benign imperialism would be exposed for what it is, mere power mongering and self interest, and the glue that holds the Federation together would come apart.
So they have no choice but to judge other warp capable civilizations by Fed standards, and interfere by offering asylum, unless there are overwhelming practical issues in any given case.
eh? In the TNG era at least, we've seen several instances where the PD is invoked in cases not involving pre-warp cultures-just off the top of my head, how about the Klingon Civil War, or the Cardassian-Bajoran conflict?
in DS9, what about Tosk?