This idea would make no sense. Let's take roleplay and logic into account.
If you sink a large amount of navy, EITC, skeleton, or whatever, then naturally a BOUNTY LOOT HUNTER will want to take your cargo.
On the other hand, there should be a few exceptions:
A) If you sink only skeletons (who will attack you just for being near them), then hunters should attack you for the cargo, but not the Royal Navy!
B) If you sink Navy only -- Royal Navy should attack; however, if you sink E.I.T.C only -- E.I.T.C Navy should attack.
Unfortunately, however, disabling NPCs from the desire to steal your cargo (not that they actually do, but that is what the game suggests) is never going to happen. Sure, this game has some unrealistic things in it, but you can't just ask the royal navy to politely not sink you for your cargo. After all, you are a pirate in the first place, which is illegal and punishable by death.
(Also keep in mind that all the current hunters are navy, so sinking them should definitely trigger warships).