Why don't your go ahead and be a little more pro-active with this and just tell her that you think the separation would be best for her right now and work on that. Tell her that you care for her and love her and that you don't want her to feel pressured in any way which is why you're doing it. She'll see that as a huge sacrifice from you and appreciate it.
Obviously all the holding on and having her in the house isn't working. Cheeseless tunnel. Open the cage door and let her free. If she wants to come back, she will. It really sounds like you have a good chance of that happening since she is in doubt.
A separation is much better than a D and it'll give you both a chance to GAL. It will probably be the hardest thing you've ever done but like they say, if you love something set it free.
My W told me flat out she wanted a D and that she was afraid to be around me, etc. almost a year ago. Now she's home in the same bed and getting comfortable. While I'm trying to slowly increase her comfort zone so we can be intimate again, I believe the S really helped her think about what she really wanted in life.
M-43 W-40 2D - 9 and 5
Emotion, yet peace. Ignorance, yet knowledge. Passion, yet serenity. Chaos, yet harmony. Death, yet a new life.
