You can't necessarily re-program an ECU that is stock from factory. There are a few aftermarket ECUs that you can buy though.
On that particular vehicle it won't make too much difference. You can tune the crap out of it, but it won't increase torque or horsepower by much.
In general from my experience the only time people tune stock or naturally aspirated vehicles is to fine tune their power output. Some Hondas actually grab some good power from an aftermarket tune. The Hyundai Delta and Lambda engines benefit decently from an aftermarket tuning as well. You would usually see naturally aspirated aftermarket tunes on vehicles that have ITBs (individual throttle-bodies), lightweight pulleys, lightweight clutch and flywheel, "Cams".
If your car is literally just a stock engine, you wouldn't really gain too much power. If it had a turbo that came with it stock, that's a different story.
This is purely from a perspective of cost versus power. It's just not cost effective if you don't want to do more work to it.
If you're going to throw a turbo or supercharger in it, or do some VERY serious engine work; It's worth it. Haltech and MegaSquirt make affordable ECU's. You have to wire them in yourself though, so if you're not too familiar with work like that I would avoid doing it yourself.
If you want a little extra noticeable performance, I would try some of the other things I mentioned above. If you're satisfied with that and want more, throw a turbo in there. If you're not interested in racing, there are alot of other things you can do to increase power that don't involve HOURS of wiring and hundreds of dollars.
If you're wondering about cost V.s. labor V.s. increase in performance, let me explain a little bit.
You can port everything that involves the intake, which will cost you around $150. You can get lightweight pulleys, which depending on the rarity of them may cost you around $40 - $80 usually.... There are extremely cheap exhausts that serve the same purpose as expensive ones. I've seen them usually around $200. You can get cold air intakes around $60 (Which is a topic of it's own).
Those are the things you could do that would increase power and response noticeably. All of that combined would probably be the same as the ECU and most likely yield more power and response. If you add all of that up you're going to spend at most $600 for a decent gain. If you buy an ECU, you'll spend $900 for VERY little. The plus side of this is that if you spend the money ahead of time doing these things, when you do decide to upgrade your ECU; It will be able to utilize the engine even more so.
As far as time for installation, if done in a single day by someone who knows cars decently; It should only take a couple hours at a time. The porting and polishing of your intake runners and heads will take a while, but it's something you can do yourself. You just need some soft Dremel attachments and some youtube videos lol.
Most of it's easy to do. If it was me on that particular vehicle, I would get all of the fun stuff first. Once you have all of it then tune it liberally =)