If siphons are restricted to the amount of fuel they suck [say 1 every 15 minutes] and the amount around a citadel that can suck, say 5 and also the fact they can be killed for a tasty killmail by ANYONE, there is certainly reasonable counter-play to it. And as a matter of fact eve is not supposed to be easy, there are ways around and if some random corp cannot be bothered to check their fuel, then they deserve to lose their citadel if that is what the result is.
You don’t leave a citadel running without checking it occasionally and if you don’t then it is your loss. You don’t even need to constantly check it, just every so often.
That is the point of siphoning them, in the hope that the defender is not prepared and that their cloning goes offline, nothing stopping anyone from physically traveling to it. Eve is hard, it is NOT meant to be easy.