Go For It!
While I saved up for my Akrapovic, I tried the following free mods on my 2009 650.
I cut off about three quarters of an inch off the pea shooter first. The sound changed very little and was barely noticeable.
I wanted a deeper tone, so I drilled quarter inch holes evenly spaced around the peashooter. I started with four, put the cap back on and tested it out. The sound was deeper at idle and the lower rpm range while accelerating. I never experienced the dreaded fart sounds, backfires, or any other negative responses.
I ran it that way for about a week or so and decided to try to deepen the sound just a little more by drilling four additional quarter inch holes evenly spaced between the first four. The sound deepened a bit more at idle and again at lower rpm acceleration. I never experienced any fart sounds nor did the bike ever backfire or exhibit any negative responses to the changes. I was pleased with the changes and would do it again. It did not sound as good as an aftermarket pipe, but it was much better sounding than stock.
I say go for it and enjoy making your bike our own. These holes are simple to fix with basic welding and you can easily weld the peashooter back on if needed.
I recently installed my Akrapovic pipe which looks sportier with cleaner lines, weighs less, and sounds incredible. Of course, it was expensive, but worth it to me.