If it does damage the rubber, then the rubber is perished and you need a new one. A rubber in good condition will stretch enough without damage. I have never seen the suggestion of boiling it before, and I wouldn't fancy trying it - though if the rubber is perished and you can't get a new one, it might just be worth a try.
Have a look at the back of the rubber you have. If the hole for the pedal is offset slightly top to bottom (some are, some aren't; it depends on the car) then the thicker piece of rubber lip should be at the top.
Jim