I think Hartsfield Landing is an episode it is good not to look too closely at, but just enjoy. For starters, the election part didn't make sense as it was a primary - of course Bartlet would win the primary. He was running unopposed for all intents and purposes. Second, the prank war escalated too far and I don't think we should really think Charlie was able to get the desk to do that.
To me, it's mainly filler. But enjoyable filler.