It sounds like she's emotionally withdrawing from you (for whatever reason/hormonal is just one possibility) She may be doing this subconsciously (not being fully aware as to why) and it may relate to her own issues of self esteem/self worth, the underlined belief that at this stage in her life romance or physical intimacy of any sort is to halt, etc.
Of course, you're correct that anger would only push her away and she'd feel justified in her behavior.
You've mentioned that there has been some counseling and that would need to be more frequent if she is open to it. Resistance and avoidance can be seen as defense mechanisms used to protect oneself. What would she want to protect herself from is another question that she would have to answer first to herself and then to you.
If possible, try to arrange for some time when the two of you can talk about what is going on with the two of you. You've shared that you feel like two ships passing in the night and she needs to hear and get that emotionally not only cognitively. If you can go some place for a few days like a B&B, try to write her a letter ahead of time that you can share with her there. In the letter, focus on the relationship as a whole first and then express how it makes you feel. Remind her of all of the things that the two of you used to do that were pleasurable and evoked a deeper sense of connection, and ask her what can happen now to recreate that. Find out what makes her heart fill with love and how is that expressed outwardly.
If she is willing, you may do things that involve physical intimacy such as giving her a foot or back rub and her doing the same, holding hands, rubbing her back, etc.
Some individuals who supplement with oxytocin which helps them reconnect intimately/emotionally with others.