Pet odors like that never really go away. We may get to the point where we humans can't smell it, but other animals can. I would suggest going ahead with the steam cleaning, but, if there is still some staining, try some OxyClean. That stuff is AMAZING! It's not just for clothes. It is for carpet, upholstery, everything like that. It works wonders. Make sure that you go with the steam cleaning. The main thing you want to do is make sure that it is sanitized. The odor may remain, but as long as the actual harmful stuff is gone, then there really won't be a problem for the little one who crawls. The only thing to do to get rid of the entire odor, though, is to get a new rug. Sorry to say, but it's true.
We had a cat once, and he would get mad and pee or poop on the carpet right in front of his litter box. When we got more cats in the house, they would smell that, even though the carpet had been thoroughly cleaned and we couldn't smell anything, and they would pee or poop in the same spot. It was crazy. We got them out of that habit, but, every once in a while, one of them would pee in that spot. So, you don't ever really get rid of the odor. Sorry. I hope this helps at least a little bit.