Like many other fun things, there is going to be a risk associated with it. However, I would rank this risk as being pretty low.
I would like to split my analysis into two sections. (1) General Health Risks in the Grand Canyon and (2) Aviation risks in the grand canyon.
General Health Risks In The Grand Canyon
You are far more likely to die of heat exhaustion or falling in the Grand Canyon than you are from a plane crash. Admittedly, this might have to do with the quantity of people exposing themselves to the elements, rather than the number who take an airplane, but the point is that all manners of seeing the Grand Canyon will have a certain level of risk associated with them.
Aviation Risks in the Grand Canyon
As you noted, there have been several Helicopter incidents in the past. However, there have been substantially fewer Fixed Wing incidents.
From what I can tell, there have been two incidents in the past 10 years with regards to aviation tours in the Grand Canyon area. In one incident there were no injuries. In the other, there was one fatality and several other minor injuries.
Try comparing that to general automotive statistics!
An air tour of the Grand Canyon sounds like a great time and the risk of injury is negligible. In fact, it might even be the safest method to see the Grand Canyon, in comparison to helicopters (higher incidence rate), Mule's (substantial number of deaths per year), and hiking (risking exposure to the elements).
In the past 10 years only one individual has died on one of these Grand Canyon air tours. I would personally take those odds and enjoy the view!