MY NO MEDICAL TRAINING I HOLD NO RESPONSIBILITY FOR WHAT YOU DO OPINION:
I have general neck problems. I would call it a "weak" neck. The ride type that I have the biggest problem with are roller coasters in the dark - namely Space Mountain. If I can't see the track and anticipate the turns, my head whips around and I end up with a headache. However, I do ride RNR (and LOVE it) but request the front half of the train because it is smoother and not so whippy. RNR is a bit brighter and so darn fast and the ride seat is designed such that your head won't get whipped so much, that I don't have anywhere near the problems like I do with SM. BTMRR gives me no problem whatsoever. TT, no problems. Star Tours, no problems. Body Wars, no problems. TOT, no problems. I plan on riding Expedition Everest on our next trip. Hopefully, that gives you an idea of what my neck issues entail.
On to MS - I have absolutely no problems on MS. In fact, we ride this at least 4 or 5 times every time we go to WDW. The ride is not jerky at all. It is extremely smooth and the G-forces are exerted towards you back rather than your butt so your head is not compressed onto you neck during the G-Forces. I keep my head against the back of the seat (it's nicely designed to provide a little "channel" for your head to rest in which also helps restrain it on the sides) and I have no problems.
Personally, the folks that need to watch out for this ride are those that are prone to motion sickness, those with medical issues that can be aggravated by stress (the ride is exhilarating) or those with skeletal-muscular issues such that even moving in a 1G environment causes you problems. If you use a walker or wear a brace, this ride may be too much for you.
Now, I got rear ended once. I was turning right and was looking toward my left checking for oncoming traffic and got rear ended. My head to whipped back and strained the muscle on the right side of my neck. I would say that it was just a little sore for a few days and only when I tried to use it. If I had gone to WDW at this time, and knowing what I know about MS, I would have ridden it. The muscle soreness would not have kept me from riding this ride.
If my neck problems were "muscular", I would ride MS because MS does not expect your neck muscles to provide much (if any) support for your head. SM expects your neck to "support" your head (keep it from whipping too much). If my neck problems were "skeletal", I would think a bit more about riding MS. If they are severe, MS could aggravate them.