Hypersmurf said:
How many rogues with tremorsense do you know?
-Hyp.
To apply the same logic: how many critters do you know for which the stomach is not a vital organ?
You might find some but they'll all be arthropods... vermins. Tough luck, the Purple Worm is a beast.
Would you consider the swallowed thief as being able to target another organ than the stomach?
And the AC argument is moot. The fact that it is hard to pierce has nothing to do with its importance to the creature. A brain is encased in a very hard armor: the skull. Nobody will argue that the brain is not a vital organ (hopefully

A better argument would have been the elasticity of the worm's gizzard. The worm's description states that the gizzard closes as soon as a creature cuts its way out. And you seem to get out to the open, not into the abdominal cavity. Thus, no (or few) digestive fluids in the abdominal cavity.
Is that enough to cancel SA damage? DM's call.
Another question you might want to ask yourself...
Since there is nothing related to this in the rules, would you consider it that much unbalanced to allow the SA?
If not, why risk an argument with a distressed player (avg 25 hp damage/round in the stomach. Not many thieves will survive the ordeal since they do about 10 damage per round without SA at their best with small/tiny weapons).