It will exacerbate TO bearing failure in alot of cars, not so much in others. Largely due to TO bearing design - most last longer than the life of the clutch, so it's not even a concern, but I know in my Legacy GT the TO bearings have been known to fail early and tear apart the transmission input shaft.
Anyway, if stop/start works upon clutch pedal depression/gear selection, then I'm good to go with it. I shift into 1st gear a few seconds before I want to take off from a stop, so the engine will be back on and won't "slow me down".
I sit at long lights/stops in neutral. No reason to have my throwout bearing spinning when I can easily observe there's no where to go in the next few seconds.
F80 m3 - 20k miles as of April 2015....08 535xit - 120k miles