While there is great potential for conflict when Chomper gets old enough, it ought to be noted that the producers are unlikely to allow any scene of Chomper turning against the inhabitants of the valley. This is a complex issue, and because it is species, not race, based, there is no possibility of Chomper being accepted if he has to kill dinosaurs in the valley in order to eat.
If this were a more mature series, it would be explored in greater detail. But since children's movies and TV series' aren't exactly good sources for the ideas of Free will vs. Fate ; Chomper is fated to have to eat dinosaurs to survive, and yet he doesn't want to eat any of the dinosaurs that live in the valley.
So far, there are two signs that something could go wrong, even in the children's series that the show is.
1. Chomper has repeatedly mentioned being hungry, which frightens various creatures of the valley (Ducky and some of Petrie's siblings have been scared of him, to date.)
2. In the very first episode, Chomper goes berserk when the cave leaks, and displays unusual strength in doing so. Imagine what could happen if he were older and stronger...
If something were to go wrong and Chomper did get out of control, the only main character who could probably stop him is Littlefoot, who by that time will be misnamed due to his mass of many tons. Spike and possibly Cera might be able to help Littlefoot as well.