I agree with you, this is a little stupid. For one thing...she's going to be in the hospital for six weeks? What?
She sounds like a paranoid first time mother. I myself have never had a child, as I'm still a teenager, but I have a lot of expierence with kids, as I have 7 younger cousins, and a toddler sister. My aunt recently had her second child, she's about a week old now, and it was a little nervewracking having all the little ones around her, but they were watched carefully and it was all ok.
It's good to be a little more careful about visitors and being out and about with the baby around this time of year, seeing as it's cold and flu season.
Talk with her about this, and tell her how much it hurts you. There is no reason that your son shouldn't be around them, if you watch him closely.
And also, maybe tell her that just because the doctors give her guidlines, doesn't always mean that if they aren't followed, the baby will die. My parents grew up without wearing seatbelts or helmets when they rode their bikes, my mom didn't wake me up every two hours to feed me when I was a baby, and yet we're alive.