It should be fine, in terms of whether it'll break or not. However, the main reason why they tell you to keep it from touching the pot is because it throws off the temp reading. Instead of taking a reading of the temp of the stuff in the pot (which is what you want), you're taking a reading of the pot itself, at least partially.
Personally, I'm going to invest in a nice digital one here soon---but until that happens, what I do (for mashing and steeping) is take some kitchen twine, tie it to the thermometer (most have a loop built in, or at least a clip), and attach the other end to the handle on the outside of the pot. I don't tie it to the handle, just wrap it a bunch of times...that way, i can adjust the height easily. You can also purchase cheap ($10) analog thermometers from bed, bath and beyond that have cool little enclosures that keep the bulb from touching the bottom.