I encourage all my students to treat their musical equipment--instruments, stands, sheet music, and accessories--as tools, rather than as objects to be tiptoed around. I say make the tools work for you!
Recently I brought in my well-loved copy of Enesco's Cantabile et Presto to show a student of mine who's currently working on the piece. I wanted to her to see how marking up the music can make it more accessible and make it feel more like your own. This is what I showed her:
These markings are from my sophomore or junior year in undergrad, a time in my life when I really went nuts with the markings in my music. I have since scaled back, but at the time it was good for me to get in there and make the music feel more like home. The French conservatory pieces are intimidating enough as it is; beating up my sheet music a little made them less so for me.
So don't be afraid to make the music work for you. If you're really not into the idea of writing all over your original, make a photocopy and just go nuts with it. You'd be surprised how much friendlier the hard pieces will become.