One_:
I seen somewhere if you don't put a wire into the RX pin until after the sketch has uploaded it fixes it, and it did!
Under the circumstances though, as described here, it can be unavoidable. I personally add and remove wires from live circuits but I usually do it after double-checking I got the right pin. Shoving something into +5V when you meant Gnd, or the wrong digital or analog pin could indeed damage things.
But with caution (and anti-static precautions) I think it is OK.