If you're only looking at things from the MGP standpoint, Chocobo racing is not for you. I'm assuming you are primarily doing that simply because that's the only thing you mention. Chocobo Racing is a two-fold system and aimed at players who seek that for the competitive racing standpoint. It has a leveling system, so the reward is NOT just MGP, but experience. As a result, the rewards have to balance themselves out. Not to mention, racing has a limited instance creation to it, so if it were the best at MGP yield, you'd run into this problem even more (probably not of much concern though).
It's hard to say if the MGP cost of g3 and 2 food is too expensive. The only point of the food is to get an edge to win, and the only real reason to do that is to gain faster experience (besides the fun of winning). Maybe it's just me, but given the point of having Chocobo Racing, it makes sense. And just to be clear, Chocobo Racing is NOT intended to be the end-all, be-all MGP source. How and why you would even think that is beyond me. Furthermore, Chocobo Racing in general is easy to abuse to obtain 1st place. Invite people to party under some level of agreement, always win. Rigged races? GG.
However, I do agree that the AFK abuse can be problematic, given the reward amount. At the same time, it's not exactly that big of a deal for legitimate players. In fact, it actually has some degree of benefit since it basically means that's at least one position better that you'll come out on (besides 1st). Unlike AFK abuse in games like WoW and its PvP, people that do it don't affect a potential hit to your personal time and reward. It also doesn't hold much weight in affecting your personal goal, which in many cases might be MGP accumulation. Unlike botting for items to sell, AFK racing isn't going to destroy an economy. Not advocating it, and definitely would not look badly upon some sort of action to prevent it (unless it affected legit player rewards noticeably), but just stating that it's not as dire as you might think... at least for now.