I think the marines are just being smart about this.
Moria already got in contact with Luffy, the marines already know that even enemy pirates are willing to join forces against them, and that Luffy already has a high arsenal of allies. they suspect that Moria will turn on them as well.

besides, they're probably going to replace the shishibukai with some 'yes-saying' pirates, with so many small pirates coming out their holes (WB being dead, pretty big power vacuum), they need forces to take care of the small pirates uprisings.
they took a guess with Blackbeard, and they won't do such things again, it's too risky for them. they only have mihawk and don flammingo as loyal guys, the rest of the pirates have betrayed them. or dead.
does Kuma-original still have a brain? or is he 100% robot?