ok first off to answer the ammo question.
my brother used to hunt deer with a 22lr when we lived in a state without ammo restrictions. my grampa used to use a 22lr to deal with stray dogs until a city ordnance banned discharging firearms within city limits. the 22 is definitely suited for cats. the twitching is just random nerves firing. a direct shot to the head will instantly kill the animal but nerves will still fire for a couple minutes after it's dead. you see the same thing with deer, coyotes, ETC.
as to the emotional part.
I had to help put down one of our dgs once. I refused to pull the trigger but I held her in place and gave her a hotdog to distract her and give her a happy last couple seconds. even with that minor roll I still felt very guilty. granted she was a beloved pet that had her own place in the family. the feeling passes, as you said yourself, it is necessary if you care for your own cats. I think of a feral cat in much the same light as a feral dog. here they are a mix mostly of various protection dogs so mix in pitbull, doberman, rotweiler, german shepherd and bull mastiff and you get the normal rez mutts that roam free. these things are a greater nuisance than a coyote. they are larger, meaner, and generally run in packs where the coyotes usually stay solitary. these are just as much dogs as what I keep in my kennels but they are no longer pets, they dont play fetch or come sit at your feet when you're depressed. they are now just a wild animal at this point.
as to the prayer. I was never one to remember them but I usually do pray at the end of the day. as soon as I get an animal I offer thanks for the bounty, if I get nothing then I offer thanks for a day away from life as usual