If you're still having issues with your neck, you should talk to your doctor and see what exercises they recommend. When you did pilates, were you doing a DVD or working with an instructor ? If you have issues with your neck and need modications, then you should do pilates with an instrutor. The same would be true of yoga. don't do a DVD, work with an instructor who can show you modifications. that may be the reason you ended up with spasms. You needed pose modifications.
Can you walk without any neck problems ? If you can walk, take a daily walk. Walking is wonderful cardiovascular exercise. there are members who will tell you how they lost 100+ pounds just by walking and watching what they ate.
You can lose weight without doing any exercise. When it comes to losing weight, what matters most is what we eat. good nutrition is what takes the weight off and keeps it off. exercise is what keeps our bodies fit. Check with your doctor. If you have physical limitations, just do what you can for exercise, even if it's just a walk each day. like I said, walking really is great exercise.