Yes, my suggestion would have been to discard the seal & dust boot and replace w/new. They work in a tough environment, and between ozone, UV light, heat/cool cycles, they deserve to be replaced.
The only time I have used a c-clamp is pushing-in pistons when I haven't removed & disassembled them.
Repeating an older post, if compressed air won't budge the pistons, I still recommend the use of a grease gun, just put a correct-size bolt into the brake line caliper hole to block it off, and use the brake bleeder to fill the caliper w/grease. It has worked every time for me if I encounter a stubborn piston. Just remember you may have to use a block of wood or two to hold the other pistons stationary, this is one place where a c-clamp to hold the opposed piston stationary may work well.
If you have the check-valve brake bleeders, do not forget to replace them with a standard open type. If you really wanted to bring the maximum hydraulics to bear, cut the end off a brake bleeder so you get the max. bore size to flow grease thru the innermost-dwelling portion of the brake bleeder.