I married a non-member while I was inactive in the church. Now that I am active again, my wife seems to argue with me when it comes to anything church related. Every time I say my personal prayers, I ask that her heart be softened, It seems like right after that I get the complete opposite and she finds some reason to fight with me about the church. I fear that at some point she might make me choose between her and the church, and I’m not willing to give up either one. Do you have any advice?
My advice is to continue to wait upon the Lord and have faith in Him, and to love your wife with all your heart.
In time her heart might be softened as she continues to feel your love and respect for her and for God. If it does then you have saved your faith, your marriage and you might even bring her to the Church. If however her heart does not soften she might just do what you fear. That would be her choice and there would not be much you can do about it. In that case your comfort would have to be found in knowing that you did what the Lord requires of you to (love her as Christ loves her) and that you can answer to God with clean hands and a pure heart on the matter.
This is the instruction that Paul gives in 1 Corinthians 7:
12 But to the rest speak I, not the Lord: If any brother hath a wife that believeth not, and she be pleased to dwell with him, let him not put her away.
13 And the woman which hath an husband that believeth not, and if he be pleased to dwell with her, let her not leave him.
14 For the unbelieving husband is sanctified by the wife, and the unbelieving wife is sanctified by the husband: else were your children unclean; but now are they holy.
15 But if the unbelieving depart, let him depart. A brother or a sister is not under bondage in such cases: but God hath called us to peace.
16 For what knowest thou, O wife, whether thou shalt save thy husband? or how knowest thou, O man, whether thou shalt save thy wife?