Genetically modified soldiers can be very loyal and very deadly, but that doesn't mean they're unstoppable or can not be defeated.
The only real reason why they had any view of being unstoppable was because they could be quickly and for the most part, easily reproducible.
If you are going to genetically engineer a species as a robotic soldier, all you have to do is start out with a physically superior species like Vulcans or Hirogens and take it from there. It is not logically realistic that ANY Human could defeat a Jem Hadar in hand to hand combat. This is not a natural species that evolved to adapt to a particular environment; they were specifically designed to be soldiers.
As I said, one could postulate that designing in an ability to quickly and easily reproduce them might require compromises in their combat strength - like designing a vehicle to haul large amounts of freight at an acceptable fuel economy is going to put serious constraints on their acceleration capabilities. Engineering is a world of trade-offs. In almost every case, designing in one particular ability comes at a cost in another ability.