Sorry, I meant that under no circumstances should you place UNREACTED thionyl chloride in the waste. It will break down to SO2 and HCl, probably bursting or geysering the container, and you will have the worst mess ever on your hands even if no one is injured.
I agree with your idea to rotovap it down, then refill with H2SO4 (a good dehydrating acid) and more absolute alcohol. Make sure your absolute is fresh and/or stored over sieves. You are basically describing a crude replacement for the Dean-Stark trap. (You don't have one of those handy, do you?)
The use of an alcohol to quench the excess thionyl chloride is okay too. I don't recall the precise procedure we used for this, so I refrained from mentioning it.
I agree with switching to a chloroform/MeOH or DCM/MeOH TLC solvent. You are thoroughly drying the TLC plates before running them, right?