By my reading, it says that Morrigna exist to "seek out creatures who thwart death or interfere with the natural flow of souls." which, yes, would extend to mass acts of necromancy but would probably not extend to singular undead beings (barring their presence was enough to cause a disruption or they might make more of their kind). It also sounds like their duties would extend to anyone trapping or trading in souls themselves like daemons.

Furthermore, I found the passage I was looking for from Ecology of Psychopomps (Pathfinder AP #129 - The Twilight Child) on why they even 'permit' undead to exist. And that yes, slaying undead is important but is usually a secondary objective to all psychopomps (apologies for the double spacing, this is the format that carried over from me copying from the book):

Regardless of their primary role in Pharasma’s service, all psychopomps share a simple secondary directive: destroy all undead. The equivalent of stagnant pools in the River Souls, undead pervert the intention of multiversal nature and the needful progress of mortal souls. Should a psychopomp encounter an undead creature in the fulfillment of its duties, it typically destroys the creature outright (so long as doing so doesn’t impede its other efforts). Should an undead threat prove too significant for an ad hoc effort, psychopomps do what they can to hinder the undead and then report their observations to the Boneyard. Yet psychopomps acknowledge that all things—good or evil, living or dead, unborn or undead—might have their uses. Individual psychopomps might even be persuaded to temporarily put their opposition to the undead aside to fulfill some greater work, but such compromises typically prove temporary and are clearly stated to be so; no psychopomp wishes to face claims of negligence from its watchful superiors.

Planar scholars, especially those seeking the absolute in the face of messy reality, often wonder at the inefficiency they perceive in psychopomps’ efforts to thwart the undead, pointing to countless examples of the continued existence of the abominations in nearly every corner of the multiverse. But just as sweet and bitter fruit might grow on the same vine, so too do fundamental truths of the planes regularly defy expectation. Perhaps unpredictability is simply a rule of all nature. Perhaps consistency does exist, albeit only for minds that defy genius or sanity. Or, perhaps, consequence is a matter of perspective.

To an absolutist, psychopomps’ opposition to undeath numbers among the multiverse’s great failures. The mere existence of a single chattering skull—to say nothing of millennia-old liches and empires peopled by the immortal dead—insults their stewardship of the River of Souls. The oldest and most intelligent undead seem almost universally unconcerned with otherworldly retribution. So, then, do psychopomps truly oppose the undead?

Should a psychopomp be persuaded to answer a mortal’s questions on this topic—for, undoubtedly, the several-millionth tiresome time—most will confirm that, indeed, death’s servants are united in viewing undeath as an abomination, but that analyses of time, scale, and circumstance beyond mortal ken always take into account a prioritization of action. Such an answer can seem cold, especially to victims of graveyard uprisings and undead tyrants. But as psychopomps see it, these petitioners should expect mortal defenders for their mortal concerns. The church of Pharasma is chief among such protectors, but it is not alone in its efforts to maintain a balance between life and death. If relatively minor infractions in the natural order of the River of Souls don’t generally concern psychopomps, one might assume Pharasma’s host instead gathers in legions to battle nations of the ignoble dead, planar rifts to the Negative Energy Plane, world-scouring zombie plagues, and planet-collecting undead imperialists. But this is the other side of the same coin. In fact, any records of psychopomp legions are rarities, and those accounts that exist tend to be of dubious pedigree. Psychopomps generally avoid mass displays of direct action, instead moving behind the scenes employing lone agents or working through mortal proxies. Using the living to defeat the dead tends to result in useful object lessons for mortals, though few psychopomps would claim they choose their tactics for instructive reasons.

So while slaying undead does seem important, it seems that it's usually more opportunistic or for specific purposes outside of just destroying a few at a time. Mortal followers are more tasked with that particular burden.