Take it one step at a time, and don't start freaking out NOW over something that won't be an issue LATER.
Your first goal when you start medical school is to do well and get into a surgical residency. While it is true that General Surgery in the past several years has had many, many unfilled spots, MOST of these were PRELIMINARY spots and NOT categorical. There were only a handful of categorical programs that went unfilled. There are also signs that General Surgery is gaining somewhat in popularity, with an overall increase in applications this year. Who knows where this will go?
Forget the supposed differences between a "great MD student" and a "great DO student." They're one in the same and both will have excellent grades, scores, letters, and some will even publish.
Once you get to surgical residency, you'll make your friends and contacts, you'll take off anywhere from 2 to 3 years and do some bench work in a lab somewhere, and then you'll go into your peds surgery fellowship. It's that simple.
Is it a little more difficult for a DO to get into a peds surgery fellowship despite all the hard work? It may be, but who really cares right now? You're seven to eight years from deciding if you really want to be a pediatric surgeon in the first place.
I know of DOs who went on to GU (Urology) residencies at some pretty top-flight locales. On my surgical interviews I've met DO surgical residents who have aspirations to do things as wild and crazy as pediatric cardiothoracic surgery.
As others have stated you are not limited by the simple fact that you're a DO. Concentrate on your most immediate goal and everything else will fall into place.
And as someone else has warned, chances are you'll change your mind. Many of my friends and neighbors, as well as I, have.
Good luck.