If it has higher resale value, you'll pay more for it now and get it back when you sell.
If it has lower resale value, you'll save money now, but have to sell it for less.
Either way, it's a wash.
I know with CJ's that automatics are rarer and more valuable. Not sure about TJs.
And yes, there is a demand for auto's - even with serious off roaders (not trying to start that debate again!). If that's what you want go for it!
The finer points of 4 vs 6, stick vs auto are debated fairly frequently around here. Feel free to join in. I don't think anyone's been declared the winner yet.