Your question is actually pretty difficult to answer since it mostly depends on particular laptop and how its cooling work. I for example have only a discrete video card an never had any problems with overheating.
In properly designed laptops, the cooling system is supposed to be able to measure the temperature and adjust the fan speed with no OS intervention. I've heard (but have not even been able to find any model numbers) that some laptops actually rely on drivers to control the cooling system and that it may not work well if the drivers aren't loaded. This definitely is troubling information. Also a properly designed cooling system should be able to keep temperature down when laptop is using the discrete card with no problems at all, but some designers may choose that low noise is more important than cool laptop, so they may try to keep the temperature up in order to lower the noise.
In my opinion the best way to be sure is to make a little test. Under windows, switch to discrete card only and run an application with heavy graphics, like computer game for example. Then check the temperature of the laptop. It may also be a good idea to touch laptop in the area near the heatsink, since the temperature sensors may not work "out of the box" on the distribution you pick. So when you switch to GNU/Linux, be sure to check the temperature after a while.
I don't see any other way of dealing with the problem unless a user of that particular laptop shows up and give us the information you need.
Also as far as I know recent versions of the proprietary nVidia seem to work fine, so you shouldn't have any problems with them.