Sending you lots of hugs, Katchie.
Personally, if it was me, I would just act as if my husband has told his family the truth and that they're in the know and I wouldn't walk on any eggshells around her about trying to hide the truth. How are you questions would be met with honesty about the struggles you've been dealing with lately with your husband and his drinking and your most recent separation.
I really hope that your mother in law is supportive of you and your boys. In my experience, my mother in law chose to be supportive of my then active alcoholic husband and enabling his drinking. With the lies he was feeding her she believed that I was the problem…not his out of control alcoholism.
I have had to since let that go. His mother is part of his support system even though his mom wasn't exactly supporting him in a healthy way, it wasn't (and still isn't) my problem.