Threat is what decides bounties, yes. But strength is a part of threat. Am I using these terms differently than the norm somehow?
Do you honestly think that Jimbei had more, let's call them "other factors" than Luffy? Son of the world's most wanted criminal, brother to the Pirate King's son. Brought shame to the Marines' two never in history overtaken facilities, Enies Lobby & Impel Down. Showed his Haoshoku Haki to everyone present at Marineford and was regarded for it as an insurmountable potential future threat. Jimbei didn't make the World Government very happy at all, but if you really think he did more than Luffy, or even nearly as much… we'll just have to agree to disagree.
I don't think Jinbe did any more-or-less things than Luffy did to anger the Government, but also remember he betrayed the government DIRECTLY. After being a loyal Warlord. Even Sengoku was surprised that he was angry with the war on Whitebeard. Luffy, it was expected of. He already gave the middle finger to them back at Enies Lobby, and he just gave them two middle fingers at Impel Down, and Marineford. Also remember Luffy was an active Pirate, and had the direct relationship to Ace. Jinbe was called to Marineford to be used as a solider for the Marines. They expected him to comply. Instead, he made a scene at Marine HQ, angry with the war, and was taken to Marineford.
The last thing the Marines needed right before a war with the strongest Pirate, his crew, and an alliance of other strong pirates, is a Marine ally betraying them.
Also we don't know how soon after the war the bounties where updated. Jinbe didn't stay on Fishman Island for two presumed reasons: Not wanting Fishman Island to be associated with him, ruining their chance at getting to the Reverie, and Marines coming to attack him at the island. This implies that Jinbe was pretty confident that somebody would spot him, and make it public he was at Fishman Island.
For all we know Jinbe had a small battle with Marines before going to Fishman Island. Luffy was presumed dead after dissapearing. Think about it like this: Luffy, Jinbe and Rayleigh came to Marineford. Luffy had his picture taken in the paper, showing him visibly wounded from the war, but well enough to come to MF. Then a little while later, Jinbe is spotted, but without Luffy. This goes on a little longer before the bounties are released, and still no sign of Luffy. Take into account the reasons I stated he should have a higher bounty, and it would make sense for the Marines to put Jinbe's bounty a little bit higher than a man that might possibly be dead.
Also remember, Jinbe's is still in the 400 mil range. It could simply be 450 mil, which really wouldn't make a difference.