How much is local blood non-Newtonian in Pathophysiology?
According to this conference proceeding blood is very nearly newtonian at normal shear rates. More accurately blood is very thick and a shear-thinning fluid, but the shear-thinning effects don't scale with a power law like other non-Newtonian fluids.

In terms of blood changing viscosities, I suspect that in living patients blood viscosity is quite constrained, not only by physiological feedback but by the fact that if the blood viscosity changed very much the patient would become nonliving. Blood circulates constantly, and when it stops circulating it coagulates(which complicates efforts to measure its viscosity, I imagine). Any local effects on blood viscosity would be 'washed away' by the fresh blood arriving every heartbeat. If there's no or very limited blood circulating to the muscular pathology you're interested in the blood viscosity is probably not as significant as the ischemic tissue death that's just about to happen.