Rem,
Right now you are experiencing one of the greatest emotional and painful situations that can be felt by a human. There is virtually nothing that anyone can say that will make your current pain dissipate. It will be hard for you to think rationally for a while but believe me when I say all is not lost yet.
You and your wife seem to be suffering from the cultural adjustment that is brought on by leaving the JW religion. Many of the things she may see in your relationship that she is trying to get away from and start anew is not directly a result of your personality but that of a personality that has been ingrained in you by the religion. Many of the things she may see as possibly controlling and unappealing could be just her observing you trying to be a good JW husband. The religion strips women of their own individuality and puts the control of their life into the religions hands and then tries to filter that control down through the husband to the wife.
At this point she does not know who she is and she is desperate to find out who the person living inside her body really is. You are in the same situation and you probably do not realize it. One of the first things the religion tries to convince you both of is that you do not have the right to be an individual and rely on your own thoughts and judgment. Neither one of you know how to really think for yourself. Right now your wife is associating "freedom of thought" with leaving "you" when that actual freedom will be realized by leaving the "religion" and not you.
You both need to learn new communication skills and spend time figuring out what each of you personally think about things in life from a completely new perspective. You have a great opportunity to share this new life together if you give each other chance to gain this new perspective and help each other deal with the transition of life in the real world.
If you love your wife and she loves you that is a very powerful force that will help both of you adjust. Setting out alone will be much harder than trying to adjust together. I suggest you think about what it is that really makes your wife feel she does not know herself. Is it YOU or is it the influences of the religion?
If you two can agree to go to counseling not necessarily with an agenda to get back together when the counseling is over but rather to begin to discover who both of you really are, it just might make you both realize that it was the religion and not each other that has made you two grow apart. The last thing you or your wife needs right now is another situation where a predetermined result is expected. You both are trying to experience some freedom. You are both confused and reacting to painful situations. Give it a little time and hold back on the reins a bit and see what happens.
Take care and hang in there, I feel for ya man.
Dave