BetterSense:
First of all, programming in C is not much harder than in Arduino. The Arduino program (which I refuse to call an IDE) converts all your sketches into C before it compiles them. However, I believe that the resulting hex code will not work on a plain AVR without the Arduino bootloader installed (I would like an answer to this).
Arduino source code is C. Well, C++ actually. The hex code generated will indeed work on a plain AVR without a bootloader. In fact, the Arduino (sort of, as you say :)) IDE can program directly to a plain AVR via an ICSP programmer. The bootloader is simply another route to get the hex code into the AVR. Once a sketch is running, there is no interaction with the bootloader. The hex code has to be compatible, after all, the hardware only understands one thing, namely AVR machine language.