Give stations and large fleets long range communications they. This way, they could send a message like "Hey, we know you're there and running without a transponder, if you turn it back on you're gonna be good.". The fleets that actually can mess with you have a way to poke you and say "hey, don't make us do something we don't want to". You turn it on and they like you, they assume you were doing something important. Turn it on and they don't like you, or don't turn it on, they'll treat you like a pirate or a enemy fleet.
Generally I think the relation between you and factions, AND the relation between a large and small fleet need to be ironed out a little bit more. With smaller fleets doing the hard labor and interacting with you more personally, and larger fleets just shouting "Don't make me come over there!" all the time until they find something that is actually worth their time.More on topic, transponder should have a different purpose for a large fleet to a small fleet and I think the AI should know that too.