Will heating water in a microwave cause deleterious changes to the water itself, in addition to killing any novel life forms present?

This is true. It causes a kind of energetic distortion and this is a part of its destructiveness in reducing nutritional activity of foodstuffs. There is a chemical alteration in many cases as well as an energetic perturbation that persists and affects the chemistry in how other molecules dissolved in the water behave. So it loses some effectiveness as a normal carrier of energy and medium of delivery for many bodily signaling mechanisms, and this will have consequences to reduce the efficiency of physiologic functioning of the body, and may give rise to illness as well because the body will not perform optimally, and being out of balance, will be more susceptible to the many other triggers that can give rise to symptoms of discord and illness that may worsen and become chronic, given a head start.