Just trying to be objective and helpful here. But I guess you could:
(a) invest in better cooling for your GPUs so you don't have to cool them down
(b) or move to a different pool with a different scoring method so your cooling periods do not adversely affect you.

For option (b), frankly most pools implement scoring methods to discourage pool hoppers. Now you may not be hopping on purpose, but you are disconnecting at various times to cool down your GPUs which will be viewed as the same thing. You might consider a strict PPS pool for that reason, but they charge high fees for a reason: it's risky for the pool and they could go out of business.

Other way to think about it, at Slush's if you "cool down" at the beginning of a round, then restart near the end, you'll submit less shares but still get full rewards as recent work is weighted more than old work. So at the end, in the LONG RUN, you even out!