Jewcy, I am "unequally yoked" and I, too, feel as if there is something huge missing in my marriage. However, I also believe that my husband is sanctified through me, as per 1Cor7:14. God has blessed me with 5 wonderful children.
God does not want to punish you, he wants to give you life in all its fullness. Micah6:8 tells us what God requires of us and it isn't slavish obedience and guilt. You love your husband, God does not want your marriage to be set aside, He wants you to make the best possible job of it and to quietly act as a witness of Christian faith to your husband. Read 1Cor 7 carefully, it should give you hope and peace.
If you pray for forgiveness, God, in his grace, forgives and forgets, He doesn't continually punish you. I think that you are doing enough of that for yourself. There is an old hymn that says, "What a friend we have in Jesus, all our sins and griefs to bear....... Oh what peace we often forfeit, O what needless pain we bear, all because we do not carry everything to God in prayer."
Prayer is often the first thing to go when we are stressed, feeling guilty or angry with God, but it is the best thing to help. I will say a prayer for peace for you, but the best thing would be if you could bring yourself to do it. God is waiting for you to talk to him, He always has time to listen and He already knows how you feel and what you want.
I hope your treatment goes well and that you find some peace, because I don't think that this kind of stress can be good for you just now.