Former evangelical here; I became an atheist during my marriage to another evangelical, and it did not harm our relationship in the least. The only reason we are not still married, is that she died.

There's nothing inherent in being an agnostic (or even an atheist) that would require "pulling away". If I had pulled away from my wife it wouldn't be because she was a Christian (or not an atheist), but potentially, if she were trying to guilt or shame or gaslight or hector or issue ultimatums to try to get me to return to the fold. This would be, not because she was a Christian, but an asshat. A Christian asshat, coincidentally, but the primary problem is that she would be impertinent, rude, and disrespectful, and to an extent, cruel, to do those things. Christianity would merely be the lame excuse for the behavior, not a necessary explanation for it. There are lots of Christians who are kind and loving and respectful. My wife was, fortunately, one of those.

So long as you are not doing any of those disrespectful things to your wife, I am skeptical that the real problem is your faith. Maybe she is avoiding addressing the real issue.

You did not indicate the nature of your rough patch so it's hard to give specific advice. Since you speak of a desire to make her "transition" easier then I assume she is what we'd call a deconvert ... she is leaving the church, and what follows assumes this is all or most of the impetus for this "rough patch".

People leave religious faith for various reasons but the common denominator in my experience is that their faith is not working for them personally and they are fed up with it. Possibly, they have felt harmed or at least constrained by it. So she may be having issues with you in a sort of "guilt by association" sort of way. The best thing you can do is give her space to work out her beliefs, do not attempt to admonish or correct or change her, and then continue to be consistently loving, accepting, kind, attentive, etc. She's still a woman and wants the things women want in a relationship. If any of your fellow believers disrespect her, stand up for her and support her. Give her the freedom of her own beliefs.

It is almost certain that she will not return to her former faith but hopefully your relationship is based on something in common other than attending church activities and studying the Bible. Continue to cultivate those common interests.

It is possible, but not a foregone conclusion, that she will try to run, not just from the belief-system, but everything that is associated with it, including you. I would not in a million years advise any unbeliever to do that to their believing spouse. All decisions of that nature should be based on whether the relationship is healthy, not on whether you agree on 100% of your beliefs.

Another thing I can't tell from your post is what denomination / sect you (and presumably, until recently, she) belong[ed] to. If for example your tribe is patriarchal, assumes women should stay largely barefoot and pregnant, then this will cause you to "grow apart" unless you're flexible enough in your own thinking to be able to negotiate a different sort of relationship -- to allow her, for example, to have a career, if she wishes to have one.

If you are a moderate evangelical or liberal Christian and a reasonably decent human, this should not be a big deal. But if you are concerned about doctrinal correctness, lest god be displeased with you, etc., then you may well be headed for trouble because it's apt to be ... challenging to coexist respectfully with a freethinker.

So ... hopefully that's some food for thought, and if you want to discuss further here or via PM I'm happy to share my perspective and experiences.

Well, if you are talking about her "transition" to agnosticism, I am not sure there is much you can do except be there for her and be non-judgmental while she figures things out in her own mind. But, does that mean that she is not really an agnostic, yet?
Interestingly, the theologian H. Reinhold Niebuhr claimed that all Christians are agnostic save for Revelation. In other words, God is incomprehensible to the human mind and without Revelation we could not be sure that we really knew anything valid about God.

I am an athieist and my wife is a christian. We get along great. We often discuss religion. We just respect each other's opinion and do not get angry about it. I respect her right to be wrong.

I lost the love of my life for the same reasons. It has been the better part of sixty years and I still miss her.

That really is easy if you don't constantly insist that she is wrong and you are right when it comes to religion. If you want to go to church then do it but don't go on and on about that she doesn't want to. Did you do the crying, etc, etc. or did she?

If you respect her beliefs and she yours, it’s possible. It might depend on how you feel about your christianity. Get educated about agnosticism and why she has come to that conclusion. There’s many interfaith or lack there of relationships. It takes work and understanding by both people. I wish you well.

My mom was christian and my dad was agnostic / atheist. They were still in love when my mom died suddenly after 48 years. It can be done.