If you use the chain breaking tool and partially remove the pin (from the inside plate moving towards the outside plate) the peened end of the pin will not be damaged. Also by inserting the pin back to the proper depth the pin can be reused on 8 & 9 speed chain. I have done this on Shimano Ultegra and Dura Ace chains. Shimano 105 chains didn't workout as well. This method of reusing the connecting pin is not a recommended procedure by Shimano or any other chain manufacturer but it will work. This method will not work on 10 speed chain. The pin on 8 & 9 speed Shimano chain is beveled on the inside but square cut on 10 speed chains.
For the vast majority of cyclists there will come a time that you will need to throughly clean your chain. Removing it off the bike (IMO) is the safest and best way to clean the chain with out possibly causing harm to other components.
I skip all the worries about pin issues and chain removal by using Missing Links or Power Links on all my chains.