Idea. On the circle of rotations Rθ=cosθI+sinθJ, the square root must be ±eiθ/2, and there is no way to choose the sign continuously all the way around the circle: this is the usual non-existence of a continuous square root of z∈S1.
Step 1: the commutant. Let θ∈/πZ. If M commutes with Rθ=cosθI+sinθJ then, as sinθ=0, M commutes with J=(01−10). Writing M=(acbd), the relation MJ=JM gives MJ=(bd−a−c) and JM=(−ca−db), hence d=a, c=−b. So M=aI−bJ is of the form xI+yJ, which we identify with the complex number x+iy (the map xI+yJ↦x+iy is a ring isomorphism since J2=−I). Under this identification Rθ=eiθ.
Step 2: sign choices. Suppose S exists. For θ∈(0,π)∪(π,2π) the matrix S(Rθ) commutes with S(Rθ)2=Rθ, so it corresponds to a complex number z with z2=eiθ: z=ε(θ)eiθ/2, ε(θ)∈{±1}. Since S is continuous and θ↦eiθ/2 is continuous, ε is continuous with values in {±1}, hence constant on each of the two intervals: ε=ε1 on (0,π) and ε=ε2 on (π,2π).
Step 3: across θ=π. By continuity of S at Rπ, the limits of S(Rθ) as θ→π− and θ→π+ coincide. They are ε1eiπ/2=ε1i and ε2eiπ/2=ε2i. So ε1=ε2=:ε.
Step 4: contradiction at θ=0≡2π. As θ→0+, S(Rθ)→εe0=εI. As θ→2π−, S(Rθ)→εeiπ=−εI. But Rθ→I in both cases, so by continuity of S both limits must equal S(I): εI=−εI, which is absurd.
Remark. The obstruction is topological: GL2+(R) deformation retracts onto SO(2)≅S1, which is not simply connected. On the simply connected set {A: A has no real negative eigenvalue} a continuous principal square root does exist (given by a convergent series).
Lesson. Non-simply connected domains obstruct continuous choices of roots and logarithms.