Imo Hatch is the real villain. He was working to sabatoge Monarch the whole time because he knew Paul's plan would actually work. Paul was a pawn, very short sighted. He never realized he was playing against his own rules. It never once occurred to him the CFR could have been a delaying mechanism for the end of time, meaning it would still happen later but Hatch new the lifeboat would work eventually, since no one had been past 2021 to see what happened. Paul screws up.
Hatch for some reason wants the end of time to happen. The note you pick up mentions as much with the whole natural time machine in Africa. I think he knows that you can change time, same as Jack also does now. So I believe his agenda is focusing on keeping the timeline as consistent as possible.
So when they play the "Africa" song...that makes a WHOLE LOT OF SENSE.