Ah I would be pissed if my mother-in-law did something with my 9 m old baby without talking to me first. I know that she has experience and that she had been through this before, but seriously how annoying is it when somebody is acting as if he/she knows what's best for your baby?!
You are a mother and you know what is best for your son! Even if your baby is ok with the pillow under his head, I think that you MIL should listen to you and do as you say, so you can have a peace of mind while you are at work.
However, my son slept flat on his back up until last month, and at around 8m he got nasal congestion, so I started putting pillow under his head (and shoulders) to keep him elevated and make it easier on him to breath. He seems to really like it. He is moving around, but his head remains on the pillow. Not once he turned around and slept on his tummy. He likes sleeping on his back or on the side.
You know, if he is just napping with the pillow, it should be ok, as long as your MIL is nearby and has an eye on him.
During the night have him lay flat without anything in the crib. Night is longer, but naps last for just so long...
Overall, I think it should be ok for naps, if she is nearby and can see him :)
mom to an 9 m old boy