Let me start by saying that this is an excellent film. That said, even its editted form is not suitable for children. I have found the rating system for Japanese animation to be very inconsistent with 13+ rated films that are okay for any age and 7+ rated films, like this one, only suited to teens and adults. Another problem is censorship. Censors are not artists and often hack out very important scenes that mar the film. Usually this means cutting out scenes of bloodshed and death while leaving the actual battle scenes intact. The result is pointless violence. Blue Submarine 6 Toonami Edition is one of these films, although the hack job is less severe than some other films I have seen, like Cardcaptors for example.
Back to the film itself: The first episode is very confusing. It is like picking up a novel in the middle and trying to understand what is going on. If you can get past the first half hour however, the story gradually falls into place and the film improves by leaps and bounds. By the end, you will probably be glad you stuck it out.
The only reason I purchased the Toonami version was that it was much less expensive than the unedited version. However, I always recommend getting the original if possible, and Blue Sub 6 is no exception.