I think the council make up their own rules, eg no caravans etc. I don't believe the council think they'll get sued at all. There's probably far more dangerous hazards on the plots than your pond, eg rubbish and broken glass that the council don't insist on having cleared up, asbestos sheds, and the spiked fencing used to keep vandals off the plots!
I wouldn't fill it in. You can always put a bit of board across it (not all of it) when you're not there. Also sloping the sides upwards, eg with rocks, bricks or timber edging so you would have to climb up it to fall in (if you know what I mean) The frogs will still be able to come and go but it means you can't fall in a hole. You could meekly agree, fill it in and no-one will ever come and check, so I'd leave it a bit and see if any notices :)