As I'm sure you've already realized, having the probe in the bottle of water is measuring the temperature of the water, not of the beer, which can be raised by as much as 10-15 degrees depending on yeast activity. You can, as you state, use a thermowell, but every time you introduce something else into your beer, you risk putting something else into your beer. If you take your probe, and tape it to the wall of the carboy, and then insulate it (could be as simple as taping wadded up paper towels to it) you'll get a pretty accurate reading of the beer temperature, due to the thermal conductivity of the glass. Keep in mind that most ale yeast activity takes place at the top, so that's where the highest temperatures will be. However, using it in a RIMS system is a totally different animal, and if you go that route, I want pictures! Good luck to you.