I wouldn't say that. You can bet your last dollar that gasoline will be the most used fuel in an automotive fuel cell. They'll just refine it better to remove all the sulpher so it doesn't poison the cell. Using gasoline in a fuel cell is ok, because it's not being burned,thus producing pollutants like carbon monoxide, hydrocarbons, sulfer dioxide etc. They will be just as 'clean' as ethanol or hydrogen.
If the carbon catalyst can be made cheap enough, they won't have to. If it would be cheaper to just replace the catalyst and recycle it with each oil change instead of removing the sulfur from the gasoline, then that's another option