I think because Sengoku knows well that Shanks is the good kind of pirate. Of course he rather don't negotiate with them, but Sengoku is a man of honour He knows how to handle in that kind of situation. Whitebeard and Ace deserved a proper burial and Sengoku understood that. If he reacted the same as the other marines he embaresses the Navy in front of the whole world. It shows goodwill and besides he didn't have much leverage. I doubt the navy could've put up much of a battle with another Yonkou and.
I think the way Shanks entered the battlefield was important too. If he started slashing and shooting it would only be oil on the fire. It was clear both sides wanted to quit but no one wanted to be first. This was the perfect solution because neither the whitebeard pirates nor the marine gave in. I think the Yonkou have a bit more rights over ordinary pirates. A bit like Schibukai, because the navy isn't very happy to battle yonkou.
So, Sengoku had a few options but I think this was the best one to keep a good relation with the red haired pirates and to prevent humilation in front of the eye of the world.
