Um, do you have any scientific support of such a claim? Not tryin' to flame, but first time i've ever heard that theory.
If anything, the disruption on each start/stop cycle is like giving the cards a mini-break.
Either way, my cards are all in the low 70s C range, and every little disconnect / reconnect only drops their temps maybe 5-10C before the server kicks back up.
I doubt this getwork failure between each coin change will cause any damage to your graphics cards. But this is what I was complaining about when I said I see getwork failures on this pool. It happens between every coin change. I have tried middlecoin, multipool and CryptoSwitcher to jump between coins. None of them have getwork failures or any delay when switching coins.
Middlecoin.com has getwork failures.... when switching.