Between the extra ground transport and the connection, I wouldn't even think twice about taking the non-stop. (Just to be sure: It is non-stop flight, and not a direct flight, right? We often use them interchangeably, but if the airline's calling it a direct flight, that means there will be a landing and possibly even a a change of plane.)
Besides which, if I were thinking about taking a 2 year old into business class, I'd have to look so carefully at the configuration, whether the car seat would fit in the seat, etc, that I probably wouldn't do it because of those uncertainties in addition to the ones already mentioned.