I'll just add my two cents...
if you want to use your reader to transfer pics taken with the camera towards the computer without plugging the camera directly to the PC, you shouldn,t have that much troubles if you reformat the card in the camera afterwards. Many people do this. However, if you want to use your card reader + SD card as a portable storage device, then use the card in the camera, you run the risk of corruption on the long run (as Gail said). In any case, always format your card in-camera before using it.
Corruption problems probably depend on the card and reader brands, rates of transfer, and other things (stars alignment maybe

)
I have used for some time a Sandisk CF card (that was formatted with the computer) with a Nikon camera without problems. When I formatted it, I noticed an increase of speed (not that much) for writing to the card. same thing happened with my Sandisk SD card and Canon S2 camera.
As for heavy use, cards are supposed to live for many many years, so as long as you use it in ONe device (as much as possible) you should be OK.