Quoting One Piece Wiki:
According to Oda, Beckman has the highest IQ of all the characters introduced in the East Blue saga. Since he is a first mate to a Yonko, he presumably possesses a great deal of strength. During the Battle of Marineford, Admiral Kizaru chose not to fight him, even though he had just fought the First Commander of Whitebeard's crew and Whitebeard himself.
We see Marguerite attacking Luffy with an Haki infused arrow here:
Benn Beckman being the first mate of the Red Hair Pirates obviously has incredible power and Haki. Since Kizaru as well backed off, it makes it evident that Beckmann can imbue his bullets in Haki as well, although that hasn't been directly shown yet.
Another reason would obviously be to avoid engaging in a war with the Red Hair Pirates/one of the Yonko. We already saw the kind of power the Yonko have when it took the whole of Marine Power to subdue Whitebeard. Needless to say, had they engaged in a war with Shanks, there would have been many more casualties.
As per the Wikia article on Battle of Marineford:
Shanks threatens both the Marines and Blackbeard pirates alike to have his entire crew involved in the fighting, if they chose to continue the war. With the Gura Gura no Mi under his possession, Teach no longer sees the point in resuming the battle and has his crew depart from the battlefield. As Blackbeard leaves the scene, the absence of a designated rival and presence of a powerful Yonko convinces Sengoku to concede to the necessity of a ceasefire, ordering the Marines to tend to the wounded.
The last and final reason I can think of is that the Marines had already achieved their goal of executing Ace and also managed to get rid of Whitebeard. There wasn't any reason to engage Beckman in the first place, unless they were looking for a needless battle.