Today, my Biztalk ran wild and initiated a bunch of Commerce Server catalog import operations. While trying to find a way to abort all of those I came across the CatalogStatus table in the product catalog database.
According to MSDN this table contains the status of operations in the catalog system. Among other things you can monitor the PercentComplete column for operation progress.
Turns out you can also abort any operation by setting AbortRequested to 1, so the SQL below did the work for me.
UPDATE CatalogStatus SET AbortRequested = 1 WHERE StartDate = GETDATE()-1