The low utilization thing isn't really necessary in the Commander. The Citation has all sorts of calendar items which can be pretty costly if you aren't flying much. The Commander really just has the annual inspection and 5 year gear and prop overhauls.
In regard to accident/incidents in Commanders, let's start with the gear. Typically, you see those gear collapse accidents when either the gear overhauls were not done (or, more likely, were just done on paper) OR they were not done correctly. There were a rash of them in the early 2000s that involved incorrectly done gear overhauls-- I don't remember exactly what the issue was. If the gear is properly maintained by someone who knows what they are doing, it is very stout and should not be an issue.
Turbulence: all of the Turbo Commanders from at least the 690 on, maybe before (not sure), have a placard on the panel which says not to exceed 180 knots in moderate or greater turbulence. The limitation is the same for the 690 and the Jetprops (840/980), and I don't think there are any issues which are worse than one versus the other. In fact, the wing was completely redesigned internally for the Jetprops, so I would be more comfortable in one versus a 690, although I'm fine in either.
If you fly into a thunderstorm, it really doesn't matter what you are flying. TBMs, Pilatuses (Pilati?), King Airs, they have all broken up in thunderstorms, as have Commanders. I wouldn't worry about it more in a Commander than in any other airplane, and I do my best to stay away from thunderstorms, especially when I see lightning strikes on the G600.
What is a problem in Commanders, and you might have picked this up, is stall/spin accidents, whether in training or in normal operations. It appears to me, some disagree, that if you end up in a spin in a Commander, it won't be recoverable. So don't go there.