My daughter has autism, which is one of the reasons I got a fish tank to begin with, so I can understand your issues (she's 4 but about the equivalent of a 2 yo)
Personally, I think having the fish is great therapy for her. I have the tanks (cause I have two now!) where she can reach them. Because she loves to feed them. Having her touch the different types of food and textures has been great for her since she has a lot of sensory issues (it wasn't great to start with!)...
Then there was the issue when I found half the food dumped into the tank!!! Luckly I caught it in time and got it out before the goldfish gorged themselves!
I can't say that there is a way to child proof the tanks, but make sure that you have time that he can dip his hands in there, and can see and watch the fish. If you make it more assessible for him, the facination will wear off sooner.
So I say as long as his hands are clean and there is no danger to the fish, let him play with supervision, and eventually he wont want to and will move on to something else. Forbid it and he will become overly obsessed with it, as you know kids like to push parents buttons!
I know everyone has their own opinions.... this is mine take it or leave it, but good luck!