Last year for over 5 months I hiked the Appalachian Trail and I did exactly what you described almost every day and never got sick.
Also what I did during that trip was to always use hand sanitizer before eating and using the bathroom and never shared food with other hikers. Passing the trail mix bag around with everyone licking their fingers after each helping is the fastest way to get sick on the trail.
In my opinion Freezer Bag cooking is the most sanitary way for a crew to cook on the trail. You're cooking and eating out of disposable, one use containers. Certainly boiling spoons in the water before rehydrating your meals should be very effective.
Look at other factors before assuming your cooking method is at fault.