The question proposed, and really the entire premise of the OP is a bit silly and misinformed. Like others have mentioned, this particular rule is in place for the safety of the long-snapper. These types of violations should absolutely be avoided if possible, if there is a legitimate risk of player injury. Sure, there's no guarantee the long-snapper would get injured in this case. Where do you draw the line with that? If a player suffers a concussion in the middle of a game, there's no guarantee he'll hurt himself any further by continuing to play. Should players with concussions be allowed back into a game if it would potentially mean the difference between a win and a loss?
It's not about preventing penalties (like the OP is phrased). It's about preventing injuries..simple as that. It's not like refs are out there telling a team if they have 12 men on the field or giving the QB a little nudge when there's 5 seconds left on the playclock to avoid a delay of game.