If you’re a player who prefers to have the flagstick out when putting, you’ll still likely use the option of having a playing partner attend the flag for you when you’re putting from distance. Should your ball accidentally strike the playing partner attending the flagstick, or the flagstick itself, under Rule 13.2b(2), there is no penalty and the ball should be played as it lies.
Conversely, if there’s a little bit of foul play at hand and that same partner deliberately stops the ball or leaves the flagstick in the hole, there will be a penalty under Rule 11.2c (general penalty). The penalty is a loss of hole in match play or a two-stroke penalty in stroke play.