Still don't understand why everyone was expecting Big Boss to turn heel after the events of MGS4, where, ya know, we find out that Cypher has been manipulating information and events for years, and we find out that Solid Snake is basically a rube being used by the AI's to bring down its enemies, namely Big Boss, FOX Hound, and Solidus, who were all trying to rebel against Cypher in the first place.
MGS4 set up Big Boss to be someone who was fighting against the totalitarian control that Zero was working for, and then wham, in waltzes Solid Snake, essentially a tool of Cypher, to mess things up.
Looking back at MG1 and MG2 and trying to parse specific dialog is going to be problematic since Kojima has admitted that as such, he needed to re-do those games to fit into his current canon.