Eli was not the first player to make a stink about potentially playing for a specific team. John Elway is a noteworthy example.
In fact, it was not unusual for players back in the day to say no thanks to being drafted by the NFL and play for AFL or CFL. Even after the AFL/NFL merger Bruce Clark said no thanks to GB drafting him in 1980.
This year there was some smoke about Caleb being ambivalent about playing for CHI, but his PR crew squashed that.
Players usually are coached by their agents to not make big stinks about where they are drafted.
Archie did pull a lot of strings with Eli and the Chargers though. IIRC SD didn't come out of the deal too badly - they got Philip Rivers, Nate Kaeding, Shawne Merriman, and Roman Oben out of the trade.