So far we have split finances 50/50 in terms of household bills/mortgage/insurances etc and pay these from our Joint Account. We have had the House valued and she has indicated that she wishes to buy me out of the house (although i have no idea how she will fund it, but not my problem), however i'm hesitant to agree or even discuss this in view of my wish to R.
You can't stop the D. Unfortunately it only takes one party to make D happen. Your attitude should be "I don't want this, but I know you do and I'm not going to stand in your way." So you don't help with the process, but you don't impede it either. So if she wants to discuss the settlement then discuss it. The conversation won't be any easier in front of a mediator. A mediator is only there to help you come to an agreement, they are not an MC and they are not going to try and stop the process. So if you can come to an agreement without a mediator then it would be in your best interests to do so.
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However, i don't want to impede or damage any potential for R by replying from an emotional state just now so would welcome any thoughts, guidance etc that would help me acknowledge, that recognises the path she wishes to follow for now. I'm starting to question whether i should just throw in the towel, give up......but i don't want to.
Letting the D happen is not throwing in the towel. You need to take a long-term view. Potential recon is way down the road, possibly years. A lot will happen between now and then, possibly including D. Giving her time and space and allowing her to pursue D is not giving up, it actually may be the most effective thing you can do to help her get in a position where she might start missing you and working on herself.