Sorry to hear you are going through this. My husband sleeps in the other room as well. He started doing this many months ago (I've lost count) when I was waking up and stupidly confronting him with questions that freaked him out. At first, it was really bad. He was super confrontational and treated me like scum. But I have countered all his hostility with love, patience, and attention. I always say I am having doubts about the org, but I will never doubt that I love him and want to be his wife. I tell him this everyday, and I work hard to prove it. My beliefs about the org have changed, and in a JW household that shifts the entire family dynamic. It will take him time to adjust and come to terms with it.
What your wife is doing to you through this ongoing silent treatment is bordering emotional abuse. (My husband has done this to me in the past as well). She is substituting her relationship with you with the org. I have seen sisters do this quite often--it's like an emotional affair--when everyone knows their marriage is on the rocks yet they insist on spending all their time in the ministry all day, everyday instead of at home working on their marriage (happens with brothers too, sadly). My advice to you is to live fully in your own home--don't confine yourself to your room. Be as loving as you can without confrontation, and keep that olive branch extended. If she is willing to go to counseling with you, I would sign up for it tomorrow. The first thing she will have to do is break her silence with you and actually work on the marriage. My heart goes out to you because she is so blind that she has someone who loves her as much as you do. You deserve to have this unconditional love in return. Good luck my friend.
