Swimming is also relatively safe. Distance running might result in repetitive stress injury, but it won't kill you.
Slow-pitch softball eliminates most of the risks from baseball. Hit by pitch and RSI from pitching are the dangers there.
Cycling removes some of the RSI risk from distance running, but replaces it with higher-speed impacts, usually into hard surfaces.
Edit: It depends on your definition of "team sport", really. If you define it such that you can't meaningfully separate out any individual performances, you're cutting out all relay-type competitions from the start. If you say archery is not a team sport, then neither is a swimming relay race. Where do you draw the line? What's the minimum number of participants that have to work together to qualify as a team?
Of the youth sports I'm involved with flag football and baseball are the two safest (especially if you're not a pitcher). Then basketball sits in the middle as pretty safe. The main worry in basketball is running into someone going for the ball. I'd put soccer and tackle football as the most dangerous (tackle football being more dangerous). If they eliminate heading out of youth soccer, it would move it into the basketball level of safety.
I'm not sure there is any way to change tackle football to make it reasonably safe for kids.
Crew, tennis, baseball, swimming, golf, all of track and field, etc.