Personally = I only hand waive droids (and other NPCs) if it fills a gap the players sorely need.
Example: a crew really doesn't want to spend piloting skills, as they're heavily ground-emphasis skill sets. So they got a droid to handle the flight dice rolls (and basically only that).
I'm sure you've picked a solution by now, but in the case of the protocol droid, if their knowledge skill sets leave them hanging high and dry repeatedly ... a freebie or debt-handout may be justified. Otherwise, they should probably earn it in game.