I have a circumcised son and an intact son, and now, years after the fact, no, it is not that big of a deal. It doesn't really matter that they look a little different from one another, and they both have a pretty good chance of growing up happy with their bodies.
However, at the time of their births, it was a very, very big deal. You know this, because you already have a little girl, but when you have a new baby, he is your world. Every little decision takes on incredible importance in your mind and you believe that everything you do is shaping your child into the person he will become. Looking back on my kids' infancy, I now believe that it's not so much the child, but the mother, who is shaped by those early decisions.
When they ask you whether or not you're going to circumcise your new baby, it's like a test. Are you going to affirm that he is perfect just the way he was created? Are you going to listen to your instinct that is telling you to shield him from senseless violence? Are you going to trust Nature/the Creator? Or are you going to submit to culture's absurdities? Are you going to buy into the mentality that it's proper to cause a child pain now in order to stave off something worse down the road--the same mentality behind crying-it-out, spanking, etc.
Most of those early choices that we make so much of probably don't really matter that much to the child years later. My husband was bottle fed and I was breastfed--could anyone tell the difference? Can you meet a first grader and tell whether she was sleep trained or whether she coslept? Can you guess which of your neighbors were spanked? Probably not. But when you're parenting, every one of your choices reflects who you are deep down, and you should be fully convinced in your own mind of the rightness of everything you do.