If you're finding TJ's with under 100k miles for about $2000, and they run and aren't stolen or a Craigslist scam, buy them...doesn't even matter what the options or drivetrain might be. If you are unhappy, I'll come buy them from you and drive 'em back to Indiana to sell them for $8k a piece.
The Sahara was (and is) the higher optioned model of Wrangler. In a TJ that meant you got a 4.0, AC, cruise, and better seats. The Rubicon adds Better axles, lockers, 4:1 transfer case rocker protection etc...but usually costs more too. If you find an SE, X, Sport or Sahara for $2k, the savings can buy you mods to out-perform a stock Rubicon.