No, you didn't hurt anything. You just spoiled yourself. You put decent speakers in there, which highlighted how crappy the sub is. Now that you're looking for the sound of a crappy sub, even when you put crappy speakers back on, the sub still sounds crappy. Give it a weak and you'll get used to it and not notice the crappiness. Otherwise, plug your computer into your home theater
Just as a small audio rant, the audio companies have bewitched people into thinking tiny speakers and a miniscule subwoofer actually sounds good. My home theater doesn't even have a subwoofer, but the front towers are almost as tall as me and run dual 12" drivers for the bass, and the sound blows modern setups out of the water. There's no replacement for air volume.