No, it is not the 'observation' disturbing the system that limits its accuracy. It comes down to one or the other. The more accurately energy is known the less accurately time actually is. If it was possible to know exactly the momentum, position would actually cease to exist.
It is also the same reason why an electron doesn't spiral in to the nucleus. Nature doesn't allow both the position and momentum to exist with 100% accuracy.
The observer is part of the system he is observing. The act of observation is a state change both physical and non-physical, i.e. Shannon entropy is reduced, thermodynamic entropy is increased. And both are part of a cause/effect chain of events.
The system is always disturbed by an observation having been made.