Enemies with Flight, Levitation, or just plain old good REF saves to avoid falling in.
It's reasonable to edit your encounters a little bit, especially if the party is becoming famous and people start researching how they kill monsters and spreading the word.
Don't negate his pit, but change SOME of the encounters to not care about it much.
Finally, a good old fashioned beat stick is a great discourager:
Sorcerer: I cast Hungry Pit on those guys there.
GM: OK, they fall in, screaming. The rest of the enemies shout "Don't let that sorcerer do it again, kill him first!". What's your AC? Oh dear, I don't think that's going to be high enough; this is probably going to hurt you more than it hurts me...
Well, it's a fifth level spell. Those are powerful. Would you feel differently if the sorcerer was using cloud kill, or feeble mind, or magic jar?
Two things: are you letting them dictate the pace of play? Can they always retreat at will? Are there safe places to rest?
A sorcerer can only do that a few times a day. Let it work. Then hit the group again. And again. Hit them again while they're resting, or threaten to.
Read this: http://www.thealexandrian.net/creations/misc/wandering-monster.html
If that fails, and it's that the party is just overpowered for the adventure, that's easy. Add more monsters.
Remember that it's only a 10x10 pit.
Which means at best only one guy is falling into it for most of Runelords, since most of what you face is Giants or similarly Large creatures.
Huge and above just kinda sit on top of it and laugh.
Plenty of things fly as well..
As others have said, the pit spells are nice, but have a lot of weaknesses. I love the spells, but rarely spend the slot to prep the higher-level versions, since they're still similarly sized with the same weaknesses.
edit- you could turn it into a game and start bull rushing their own members into it.
Use Bull Rush or Awesome Blow to put the party in danger of suffering the effects of the spell. Add the spell to the spell list of some enemy casters (they all pretty much use Core spells exclusively, which puts them at a disadvantage anyway).
Also, with the high number of large+ size monsters in Runelords, there should rarely be more than one enemy in the area of the pit. Just add a few more foes and the Sorc will run out of spells rather quickly.
And don't forget that all giants can throw rocks. If they see him taking out one of their number with a single spell, that's guaranteed to draw their attention. Keep him on the defensive with a hail of thrown rocks.
Large enemies usually have a low Reflex Save. You could take a useless feat from each enemy and replace it with Lightning Reflexes.