IMO (being old enough to have ridden with both) I think clipless is MUCH safer than toe clips - for the simple reason that you can get your feet out without using your hands. I think the choice should be between clipless and platform pedals - not between toe clips and clipless.

If your main concern is your foot pain, you can get MTB shoes that will work with platform pedals. The soles aren't as stiff as road soles, but they're way stiffer than "sneakers."

I guess my main concern would be how much ROM you have in your bad ankle, knee and hip. If they're hypomobile, you may have difficulty getting out of any pedal that holds your foot, clipped or clipless. OTOH, if they're hypermobile and weak, then maybe you're in extra danger of your foot slipping off, and it's best to use a retention system. Is it possible to ask your PT about this?