My take on the whole Belize thing
As someone that owned a home and spent a lot of time in Belize (mostly in San Pedro), here is my opinion of what happened:
The raid on McAfee's compound on the mainland (I've been there) was punishment for not contributing to some local politicians campaigns. The whole raid severely pissed off McAfee. Remember, he "donated" a bunch of laptops to some senior government officials previously. This being McAfee (and I think he even eluded to it in an interview), I would expect he had backdoor access to all of these laptops.
After the raid, he decided to make use of some of the dirt he had on the politicians. Or, at least he threatened to. This being Belize, they are even more corrupt than your average dirt-bag politician, so I'm sure there was plenty of material.
McAfee had a nice beach house in a fairly remote location on Ambergris Caye. There was a report of some guys in black wetsuits that came ashore in the middle of the night on a rubber raft and killed his neighbor. Again, this being Belize, we're not talking navy seals here, just a bunch of goons hired by the politicians that McAfee had by the short hairs. The problem is that they got the wrong gringo. Give them some slack, all of those beach houses must look alike from the water in the middle of the night!
The last thing McAfee wanted was to end up in the hands of the local police. There had been several cases of suspects "mysteriously" dieing in police custody about this time. McAfee knew what would happen to him if he tried to cooperate.
When he landed in Miami he was taken off of the plane by FBI agents. The agents interviewed him for a short time, and then offered to drive him to wherever he wanted to go. The only way the FBI would let a murder suspect off the hook like that would have been for him to give them some of the dirt he had on the Belize government, and thus be able to prove he was set-up.
This is all just my opinion based on pure speculation and my own experiences in dealing with government officials in Belize. I offer it as a possible theory...