Killer's bounty was 162, higher than any strawhat other than Luffy at the time, and Kidd was his captain, so… and again, lots of civilian casualties. I don't know why you find that a hard reason to grasp.
For all that Luffy did crazy unprecedented things, every time they can point to the fact that one of his crew/family was at stake. He never attacked a government facility just because, he never hurt anyone except those that attack him, and he's on record as saving people. Plus the government knows that he did their work on the Buggy, Kuro, Arlong, and Crocodile problem... and they DON'T know about Skypeia and Enel, Luffy's bounty might have been a little higher in that case, though they obviously covered up Moria. Plus, again, Buggy took most of the credit for organizing the Impel Down scenario.
"Here's this guy saving civilians in every town he visits, taking down problems we weren't even aware of... but he beats up our guys whenever we harass him first."
"Here's this guy murdering civilians in every town he visits, and going out of his way to kill our troops whenever he sees them."
There's a vast difference there. Purely from the standpoint of, if Kidd actually kills Marines, but Luffy only beats them up, that's a vast difference in threat, if not actual power.
Of course now they've overinflated his bounty like crazy and are giving him more credit than he deserves, sort of compensating for Buggy's earlier credit hogging and missed details.