A "better" way? That's subjective. Your code will likely be smaller, faster, and more efficient. But far more complex since you have to do everything yourself like setting up timers and registers, and such. If you use libraries over there, you run into the same issue anyway (though it will still likely be smaller code).Arduino is great because it is simple and does a ton of work for you and hides all the really scary bits. But you sacrifice on code size. You are trading some things for another. In the end, you can actually just write the same code in the arduino IDE as you can in AVRStudio. Both are using avr-gcc as the compiler. You can access everything directly if you want.
Or you could write the source in any text editor and build the image manually - you don't *have* to use an IDE.
Obviously you aren't going to save 1.75K by removing it because many of the same support libraries are used by other functions
Not that I said anything truly profound or magical, but it is stuff like this that should really be put up somewhere with tips, tricks, and gotchas. With the arduino, it is so easy to use libraries. I try really really hard not to unless I understand completely how they work just to keep my code from getting bloated. Even when I am well under the 32K and 2K marks, I still loathe the idea of wasting space. I guess that comes from the Commodore 64 days.