We have a cardboard cover over our locked cat flap at night but this is mainly so our cat doesn't sit staring outside all night at what he's missing. If I was worried about other cats getting in despite it being locked then I would just shut the kitchen door so it couldn't get in to the flat.
And yes, what you're suggesting would be cruel. Squirt it with water if you see it in your garden by all means but of course you don't imprison and then spray a cat, it's not going to understand!
As for the cat attacking... well they do that. My cat is regularly chased and ganged up on by all the local cats and my stance is he needs to grow a pair or learn to run fast... thus far he's a damn fast runner! ;0)
I think shutting the kittens in one room at night is probably the way forward for you at the moment.