Hrm, I don't remember for sure, but I was pretty sure that you could remove the carpet without taking the seats out... If memory serves me, there are just a few snaps around the base of the seat to connect the front and rear sections of the carpet. In fact, I'm almost positive that you don't have to take the seats out, at least you didn't in a 97. I can't see them changing that...
As for not putting a liner in right away, I had my carpet out for about 4 months before I rhino lined it, and there were no problems. It's a little louder, with road noise, and you can feel the heat from the tranny tunnel/engine compartment a bit more, but not that big a deal. The only problem I encountered was the floor mats kept sliding up under the pedals, so I would recommend tying them down to the drain hole in the floor so that they can't more, or just going with no floor mats at all (That's what I did.) The tub will definetly get some scratches from you standing on it with all the gravel and crap that will get in there, but you have to rough up the paint to apply the rhino liner anyways.
If I were to do it all again, I'd spend less time waiting to take the carpet out - It's great being able to spray out the jeep as soon as you get home. Whatever you choose, good luck and have fun with it!
Adam