hmm... there's two different things that I think you might be saying, and I'm not sure which one it is.
1) the divergence in spherical polar coordinates has 1/r terms, so we should not be allowed to take the divergence at r=0 using spherical polar coordinates.
2) with a non-zero r, as we take the limit of r tends to zero, the divergence of the Poynting vector will diverge to infinity.
now, 2) is only true when we have a point source. This is the case for the solution in the O.P. This is a wave created by a point source, so close to the point source, there is an infinite amount of energy transmitted per volume (in loose terms). But 2) is not true when we have some finite charge distribution that causes spherical waves. In this case, the divergence of the Poynting vector is always finite, even when we allow r to tend to zero.
As for 1) yeah, I guess that is true. But this is not a fundamental problem. We can just switch to cartesian coordinates for the case r=0. So if we have a spherical wave that is created by a finite charge distribution, this will work, and we can calculate the divergence of the Poynting vector at r=0. And if our spherical wave is created by a point source at the origin, then again, quantities will diverge to infinity when we approach r=0.