Looks like deleting a shelf calls the script
/AW/Maya4.0/scripts/others/deleteShelfTab.mel.
I opened that up and it is really easy to see where it creates this prompt. I would just comment those lines out and make sure the script is auto-confirming and then rename the proc/script to force_deleteShelfTab or something to that effect.
Digging through that script a bit more it looks like the nuts and bolts comes down to one line...
deleteUI -layout ($gShelfTopLevel + "|" + $shelfName);
That will delete a shelf, but I would take a look at the other stuff in there in case there is anything important. It looks mostly like shelf auto-backup code, though.
--JeffD