So sorry to hear this. As a teen I can completely sympathize with your boys, my mom walked out on us when I was a teenager. At the time it was because SHE was running away from the JW's and my dad who was abusive. Although at the time I hated her because she took most of her anger out on me, I couldn't help but feel abandoned. If my dad was as bad as she said, why would she just leave us with him? It was a very confusing, hurtful time.
But even though I felt that way I was relieved to have her gone. No more waking up to shouting matches, no more tension, no more verbal abuse. My home finally felt peaceful and after several months when she wanted to come back my dad asked for my advice. Now why he asked me is a completely different trauma but I do remember whole-heartedly saying NO. I couldn't imagine going back to the way things were. And thankfully they divorced shortly after.
Your boys are hurting right now and they have every right to hurt. Even a bad mother is better than no mother and although it sounds like they are done with the JW's the guilt feelings are still there. The feelings that you are a horrible person for leaving, even as a kid those messages creep into your mind after years of meetings that try to scare you into staying a JW. That their mother has mental health issues is of course a completely different issue and would be hurtful on its own. To combine the two has to be painful and again I am so sorry for all of you.
I would definitely look into counseling, they need to be able to work through it and as a teen who went through my own pain at that age, I can say that self-medicating with alchohol and sex is very easy to fall into, I am just thankful that drugs weren't an issue although I am sure I could have easily went there. Your being there for them is the most important thing, even though they are teenagers it is very easy to fall into child-like feelings during difficult times and knowing they have one steady, healthy, strong parent will no doubt bring them much comfort. Hug them often and take care of yourself as well.