Are the squats body weight only?
There's no reason why you can't use the leg machines at the gym providing it's pain-free for you. Bear in mind the machines only work a couple of muscle groups, whereas more global exercises like squats and lunges work more, muscles and are more functional. for returning to running.
I'd definitely add some lunges to your rehab - especially dynamic ones. With your feet hip-width apart, take a long step forward and then drop the back knee to 6" off the ground. Come up a bit from this position then using the front leg push yourself back to the start position.