I think we can rule out the skaven, there is no Ubersreik undercity anymore, so getting the barrel of powder from there would require going out of their way to acquire it, when a framework using normal gunpowder could work as well, easily acquirable in the same process of getting the barrel. the fact that shots were fired also disqualifies the skaven, at least their direct involvement, since the flash would allow any survivor to see the culprits, and thus risking the whole operation.
the direct culprits were human.
The best powder is apparently now sourced from Ubersreik, so even not Marienburg aligned mercs would probably get it from there, specially if they are going for hard targets, the location being close to Marienburg may then be just coincidence.
The framework theory is not very sound, none of the materials are actually sourced from Marienburg and they are only suspect because well, they are suspect, it's the context of the riverine trade war that makes us think about them at all.
so, I think the most likely explanation is Marienburg paid mercenaries to disrupt the canal efforts, but did not micromanage how to do it, mercs being mercs they decided they had a chance to take down a big target (maybe after seeing the "new" powder in action) and took it, expecting a larger payday.