I also faced the same problem with Transmission > 1. As you suggested renormalization of transmission by dividing with Purcell factor. Renormalized_T=T/PF, where source power will be replaced by dipole power. The problem with the division is it will give the maximum values if T and PF both have nearly the same values. It does not matter whether the values are small or larges. For the diameter sweep of the dielectric, I found T=0.067 and PF=0.14 at 100 nm dia of the structure, and at 300 nm dia, I got T=0.98 and PF=2.31 leads to a maximum transmission, while doing renormalization I am getting Re_T= 0.47 for 200nm dia and 0.42 for 300 nm dia. Which seems to be an illogical situation. 

Maybe renormalization is a solution but should we use some kind of filter like renormalization is necessary only when PF>1. Please comment on it. Thank you.