Kizaru was aiming an attack at Luffy and Law. Beckman pointed a gun at him, and Kizaru leapt into the air and attacked LAW'S SUBMARINE. He never attacked Beckman or any other member of Shanks' crew.
The balance of power didn't exist back then. It wasn't until the Great Age of Piracy, started by Roger's death, that all this came about. The World Government is the one that wants the power to exist, as evident by the scan I linked.
The death of One Emperor caused a massive power vaccuum as shown in the scan below.
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Why would the Marines let this happen TWICE?
Because this led to an insurgence of piracy. Roger starting the rumor that One Piece existed led to the Great Age of Piracy. The One Piece wasn't something that was confirmed to have existed until WB said it, and that caused an increase in piracy, as shown in the following scan.
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They never said this about Luffy. Akainu wanted to kill Luffy because of eugenics, him having the blood of Dragon.
You have zero proof of this when there's more proof that fighting Shanks carried no benefit to the Marines.
Except he beat Whitebeard in his best state at Marineford.
Rebuilding Marineford has nothing to do with the balance of power falling if they defeated shanks.