I agree with Denise; try including her in a future event and let her know she will be included.
Ultimately, it will be up to your mother-in-law to get past this. I don't know if she'd appreciate it, but perhaps sending her a heartfelt card and some flowers would soften things a bit. "I so appreciate how much you care and love your grandson. This choice was made only because my mom is retired and we didn't want to move our son back and forth between houses while we were gone. However, we would love if you felt like taking him for an overnight or two before the baby comes. We know how much he loves spending time with you, and I love that you love spending time with him. Hubby and I having a few date nights alone together would really be nice."
This puts the ball back in her court, gives her confidence that you trust her without your direct supervision, and keeps you "in the neighborhood" should a medical concern arise with your FIL. At that point, you've made a lovely gesture to her and she can respond positively or continue to feel slighted. But you've certainly made it clear that it wasn't your intention to slight her, after that, it's up to her.