From my experience, once soil gets really mucky like that, it'll be hard to get rid of the smell. It might die off if it dries 110%, but it'll retain the smell in the tank as long as it's wet. I'd remove it. I wouldn't give up on soil altogether, though. Try keeping it dryer. Aim for the moistness of a houseplaint. Maybe you could use moss for the really wet, end that's under the water line. That way, it would make for easy removal if it gets a little funky. Also, remember that those earthworms can drown if it's too wet. It's possible that some of the funk is coming from a drowned worm or two.