Ok…I do see something wrong with your MIL walking into your bedroom but I dont see anything wrong with your son walking out of the bedroom and spending the morning(s) with his Daadi. What’s wrong with that? Your MIL wants to spend time with her grandson. I say…take advantage of it!! Take that as an opportunity to spend some alone time with your hubby 
and/or sleep in.
As far as your MIL interfering …how is she interfering if all she wants is to see her grandson in the morning? Let her have him in the mornings…that doesnt mean she is raising him. Imagine how happy she would be if one morning you walk out of your room and ask her to watch him while you sleep in a little longer. After that..he is all yours.
You know…I bet if it was YOUR mother living with you and doing the same thing…you would not have a problem with it. Be honest with yourself…and think about that.