It's not that the popup flash is to never be used, it can be a tool if used correctly and in the right context... What it is intended to be is a fill flash (fill in the immediate shadow detail). It isn't quite powerful to use anywhere beyond lets say 10 feet, and hence there is the misconception. Now even if you get a speedlight, and you plan on shooting with it on camera, you are basically using a more powerful pop up flash in that it's coming from the same direction, same purpose, just more power... tool time anyone? Now if you take the flash off camera, I'm not sure if your camera has a PC out cord or not.. but if it does, you can use your pop up as fill and your flash as an off camera key light, which is the ideal situation. Whenever you upgrade, if you decide to upgrade to the 60D or 7D, you can then use your popup flash as a wireless commander and use the popup as fill, speedlight as key, and then you could even then be more creative, use umbrella, softbox, etc for your speedlight. I've even used a makeshift diffuser on the popup to soften it and make it more functional as well as keep the commander function with the off camera speedlight.
With your camera, you may be limited on what you can do with your pop-up and or speedlight, but if you can use both, then you could have the best of both worlds. If you can only use your flash on camera then you wont be getting anymore than a popup flash on steroids. If you can somehow get your flash off camera, you could be more creative, but depending on your camera you may want to some how add a fill light if possible or use reflectors to fill in the shadow areas.