Another vote for just using what you have.

The conversion to flat bars isn't terribly hard, but it isn't really an improvement and it would mess up the fit of the bike. For five miles any bike will do, including a really nice bike. If you don't want to use your road shoes, put platform pedals on it. If you feel that your riding position is too agressive, get a stem with a steep rise angle. If you find that you get flats, buy some new tires.

I wouldn't spend any money on it at all until you're excited. Most of us here love riding our bikes to work. If you don't, chances are that you won't stick with it. If you end up loving it, I wouldn't be surprised to see you getting the Defy back out on weekends.