I don't know how much fire skulls would have helped you at Limbo. It definitely would have melted a majority of the corpses, but I think you'd still have some opposition to deal with, like viles. And whatever the viles revive.
My experience with Limbo is that, the easiest way is to simply knock things into lava. Shotgun, rocket launcher, pistols with SoG 3+, whatever. But you still need some way to deal with fliers and viles, because they're not affected by damage tiles.
I do that too, though--if Agony Elemental drops fire skulls I don't pick those up. Well, I pick it up to have it count to my list of collected special items, and then I drop it immediately after and move on.