Hello Sanchy!
Contrary to the urgent type of thinking in the organization, you really do have all the time in the world to think these important issues through. There is no race to the "finish" line.
You are very nicely attuned to your wife's wellbeing and sound like a considerate, respectful mate. Your wife expressed a sentiment that had more than a grain of truth in it: She married you when you were a committed Witness who submitted to the direction of the organization. You've now changed - albeit in a manner where you are attempting to cause the least disruption to others. It is a shock to a spouse when their mate begins to express ideas that go contrary to what they once believed. Even to express doubt suggests a change of sorts is occurring.
What will "save" your marriage is the love and goodwill between you and your wife. She needs lots of reassurance that you are still the same husband she married in terms of your love and commitment to the marriage and your children.
I know I am not saying anything new here - and that you are already proceeding with the utmost care. Stay around this forum - it is possibly one oif the most tolerant, accepting forums for those struggling with doubts and/or trying to find a constructive way forward.
Realizing one's cherished beliefs may not be "the truth" can be disturbing - but it can also be gently "freeing" so that you begin to consider 'where to from here'. Best!