Before getting my Riot, I was considering buying a "basic" model that didn't come with anything (like yours). I researched the cost to install power windows and power locks, and this is my conclusion:
Power locks can easily be installed using actuators. Most shops can do this for about $50 or less per door, give or take a few dozen bucks. Of course, the alarm itself will also become a big factor in what the total "system" would run you.
Power windows, that is expensive. You have to buy aftermarket power window kits (couple hundred bucks), then have the motors, wires, and switches installed (lots of man hours).
$1,000 for the whole thing is pretty much reasonable and with most cars, from the manufacturer, that's how much it costs to upgrade to power windows and locks anyway. I don't know why Jeep doesn't let you just choose power windows/locks as an option, without upgrading your model. Luckily, I got a Latitude, which is a 4x4 sport with Limited features.
I negotiated the hell out of my price, got rebates, incentives, good APR, and put a ton of money down. I have heated seats, heated mirrors, remote start, power everything and a bunch of other crap I never even use, but I got it for the price of a basic model, almost.