You are right, it's fine for her to be uncomfortable with this scenario. You want reconciling to look more comfortable than this.
She took a step toward you by asking how you're feeling, and I don't think you drove her further away with your response. I'll be curious to see how she responds. It's great if you can suppress the male "fix it" impulse and instead make these dynamics a joint challenge to be discussed.
I'm sure she would love you to beg her to come back, but that would just make her feel more comfortable staying away. Keep doing what you're doing -- make her wonder, make her want to know more. Show her happiness and self-confidence. Bring back the man she married. Most importantly, address the financials!
You can turn this around, you're doing fine although you may not be able to see it. Keep pushing yourself to do what you need to do. This pain and angst is a rare opportunity to have the motivation to improve
Accuray
Married 18, Together 20, Now Divorced M: 48, W: 50, D: 18, S: 16, D: 12 Bomb Dropped (EA, D): 7/13/11 Start Reconcile: 8/15/11 Bomb Dropped (EA, D): 5/1/2014 (Divorced) In a New Relationship: 3/2015