I'm sorry to hear about the new pain. That also happens to me whenever I do any kind of exercise or even stretching for more than 10 min. I really hate that they say
"you should be able to go back to normal activity" at such an early stage! Your only 3 mos. post op and Pilates seems kind of extreme and hard on the neck to be doing at this point and time. I would just walk if you can and let pain be your guide.
I had the same exact situation as yours (except for the other way around) and had herniations also on C6/7 and C5/6, and they also (as a conservative measure) took out only the one level (C5/6), but then not even 9 mos. later C6/7 had to be taken out too. Soooo please take it very easy and be careful, because the discs around the one that has been removed will try and overcompensate for the one that is gone, which could make them weaker.
Also I had the same pain after doing exercise. Ice packs on my neck helped quite a bit and taking ibuprofen. And like everyone here keeps reminding me "Rest, Rest, Rest and more Rest (if possible anyways). Just keep an eye on it and I would let your doc know what happened.
Take care!