I have to say honestly Ice you hit the nail on the head.
I can already say that a huge amount of game time in the stallion-grad game has been spent arguing about what is the right thing to do. and that was when karma did not ever DO anything, adding in how integrity will effect a lot of things, and provide massive bonuses will make it all the harder for a party with diverse virtues and ideals harder to play. And i can honestly say that lots of parties do tend to get dragged along one set of PC ideals and morals unless the other players are willing to go "ya good luck with that I'm going to do my thing instead" or just give up several points of valuable integrity to not waste game time fruitlessly arguing about what to do.
Also as some have stated, forcing a player to play a virtuous character based on a one word [which is entirely possible for them to not know what their virtue even IS at the start of game] by dangling some potentially massive bonuses seems like a bad thing to me. The feeling that a player/pony is ONLY doing something because it gives them bonuses doesn't seem right for a system proposed to "make all players play their virtues like its the most important thing about their characters" when, right now, its the least important thing 90% of the time.
Is it possible for a pony to loose their virtue and gain a new one even? It's very possible character growth for a pony to hit a low end, and find that the virtue they thought they had was in fact not right. If you want everyone to simply play a hero for bonuses then yes its a fine system that will work well as long as DM's and players manage to nail out exactly what they consider is virtues for themselves and are willing to split the party at any opportunity to avoid loosing any of that tasty virtue points.
Ask me about shamanism, i can FAQ it for you.