The Temporal Cold War stuff was forced upon the show by UPN and really doesn't make any sense. The thing that really bugged me was the ridiculous gymnastics they had to go through to make it somewhat plausible that Archer would ever actually need to be involved, it never was.
I think your making the right decision in pushing through season 2 but be warned that most people consider it even worse then season 1 but however bad it gets just know that seasons 3 and 4 are much much better.
"Well, I come from a long, long line of smartasses. Smartass is allergic to dumbass. Itís actually a physical allergy, as in youíre repulsed by dumbasses."