I suppose this depends on the severity of the subject matter. Since everyone is using the comparison (despite how irrelevant and stupid it is) of telling a police officer if it was alright if a "friend" were to commit "x" crime for "y" reason, under "z" circumstance.
In most cases the answer no can be given and no further action would be necessary, however depending on the nature and severity/threat level of the question can prompt further action.
I suppose in this unfortunate case, this GM got on his high horse and felt you were up to no good to commit one of the highest policy violations in the game: using unofficial third party tools.
Yeah it was *** up and probably unnecessary, but his actions nevertheless were indeed justified.