To actually answer your question, no, this will not damage the gun. The sear deactivation lever (and instruction to use it in the manual) is simply S&W's way around liability in case you don't have the sense of mind to check your chamber each and every time you disassemble your gun.

Rule #1 to disassembling a firearm: personally make sure it's chamber is cleared and ammunition is removed.

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M&P40c/15-22/SD9VE/Mossy500