I'm glad you are sticking to your original idea for your son to practice Judo and not being swayed by other "more flashy" martial arts, which don't necessarily equate to being more practical.That is my thinking. There is no such thing as "safe" sport, unless we are talking about chess (but I'm not sure it is actually sport at all).
My reasoning behing trying to start him young in sport is not actually connected to martial arts as such. I want him to develop mentally and work on his confidence, which will be very important later in life. It has nothing to do with beating other boys or anything like that.
Not taking away anything from other martial art sports, I think Judo has a good balance between mental and physical development. Self confidence and respect for others are the basis of everything in Judo. I also think it is a good start up sport, one that he can stop at any point and start something else. I also want to instill in him the love for sport and love of being fit from a very young age. He already is very fit for a small kid and loves all kind of sport (and I'm not talking here about watching them on TV). He also has lots of energy which I would like to channel.
The only problem I have is to find the right class / trainer for him, one that will not only show him how to throw somebody on the ground but also work on mental development as well. Knowing him, I think best for him would be a small class of same age / skill kids and a trainer who loves and knows his job.
Obviously judging by my profile pic you could say I am slightly biased towards Judo however I did Karate for many years as a kid and then went on to study and teach Kung Fu. I now practice, almost exclusively, Brazilian Jiu Jitsu, but I'd still recommend Judo as the prefect Martial Art (technically its a Martial Way ) for kids to learn and one that should he continue to practice in to his teens and adulthood, will become an effective form of self defense, unlike a lot of traditional martial arts that do not have full contact sparing as part of their training.
The founder of Judo, Dr Kano, saw Judo as more than a physical Art. It was introduced in to the school curriculum In Japan as a way of teaching the body and mind. I believe he was against Judo becoming an Olympic sport, despite being part of Japan Olympic committee himself.
anyway I digress. I hope you find a good club soon.