Keep the vented loop, replace the check valve
The vented loop prevents waste from the tank from backing up into the toilet when you're heeled enough to send it back into the toilet discharge line. There should be an air valve in the nipple at the top of the loop that only allows air IN, nothing out (which, btw, also eliminates the need to vent the loop to the outside of the boat). Yours apparently is either missing, needs cleaning, or needs replacing. When the loop is working the way it's supposed to, there should be no odor from it. Or, the loop may not be the culprit...it could be hose that's become permeated with odor.