I had the same problem with the severely damaged piston in my SRX engine. The piston was distorted due to a lean burn down. I could get the wrist pin circlips out but the pin woud not come out with a wrist pin puller, even after heating the pistone with a propane torch. I had to use a dremel tool to remove the material from the piston in the circlip area. The pin then came out with the wrist pin puller.
Whatever you do, you do not want to put any force or load on the connecting rod.