I wouldn't be too concerned about it. Exposure is the fundamental thing for a child of that age. As Todd says, it's difficult for a 3-year-old to develop habits at all. It would take a lot more attention span than a child of that age has to be able to develop a repetitive-motion injury, in my opinion.
A child with talent will typically spend time listening to how the notes interact, playing two notes at a time, that sort of thing. When you see that sort of concentration, encourage it. That same child will also spend time banging around as well. You can usually tell if he's getting frustrated, and when he is, distract him.
If you're going to be the first one to teach him, I would recommend that you familiarize yourself with the Suzuki method (although I wouldn't fully embrace it). Traditional teaching methods (teach reading from day one, starting with middle C, quarter notes and 4/4 time) generally aren't very effective with children under the age of eight or so. There are just too many things to learn in that method before a younger child can dive in and start making music, and they tend to get frustrated and tune it out.
The Suzuki method emphasizes the idea of a child learning music in much the same way that he learns language, through imitating what he hears. However, practitioners often go a bit too far in that direction, to the point of de-emphasizing reading music. It's not uncommon to see older Suzuki students who play with better than average technique, while having worse than average reading skills. So I would read up on it to get some ideas, but I wouldn't recommend that you put your son in a Suzuki class.
Once a child starts talking, he can start trying to play music, too. Once it's time for him to learn to read, he can start learning to read music, too.
The traditional method books which I use with my students are the Alfred books. If you pick up the very first one (Prep Course: Lesson Book A), you should be able to get an idea of when your son can get use out of it.