Would accessory charging via USB hurt a MacBook Pro?
Not really. 

The rating of your MacBook Pro battery is 1000 full charge cycles and you probably get 500 charges of your Bluetooth per one discharge of the Apple battery, so you’re taking 1 / 500000 or the equivalent of diluting alcohol in water at two parts per million. 

If you do the milliamp hours calculation for your situation, that’s more accurate than my estimate, but if you factor convenience and the eventual cost of a new Apple battery, I can’t imagine anyone not charging some devices unless your Mac battery already has issues unrelated to charging Bluetooth devices.