I just killed all the legionaries at Cottonwood Cove, came back to turn in the quest, and as soon as I fast travelled anywhere from there, NCR behaves as hostile toward me, even though their standing in Stat is still on Accepted. What's going on?

Is there a way to debug the situation using the console, see what condition checks result in hostility? Even if I setreputation 000f43de 0 0 and setreputation 000f43de 1 80, turning myself Idolized, all NCR still behave as hostile. Other NPCs don't.

My gameplay is basically completely ruined. Any advice would be greatly appreciated.

You can try some of the console settings listed here-

http://fallout.wikia.com/wiki/Fallout:_New_Vegas_console_commands

Specifiably perhaps "remove from all factions"?

Hope it helps.

I haven't tried that one, will do. Is there perchance any commands that I can use to *query* current state of variables and reputation etc.? So that I can go and look up what about the current state is causing these bugs.

I'm certainly no expert but if you have the time you can look through here -

http://fallout.wikia.com/wiki/Gamebryo_console_commands_%28all%29

Some are self explanatory, some are annotated but most I'm not sure of (and also haven't gone through all of them yet).