I waited too long to get a divorce. Once I went through with it, I have never regretted it. In fact, I have never met someone who regretted a divorce. I think human nature is to hang on too long to a marriage that clearly isn't working.
I moved out from my house when it was clear that things weren't going to get any better in my marriage. I started sleeping in the living room a couple of months before that (way too long in retrospect). At this time I was trying to resolve things and didn't want a divorce. I was trying to get marriage counseling.
After a couple of months of physical separation, and a chance to sort out my emotions, I decided that the marriage was over.
Some thoughts. Divorce is hard for everyone involved. You do it because you want to get it over with and you know that things will be much better once it is over.
Once you decide to divorce, you are not responsible for the mental health of your spouse. You should be kind, but she is an adult and she needs to find other people to support her. Your responsibility is to pick up the pieces of your own life.
I disagree with your therapist. Once it is clear that the marriage is not working (and it sounds like it is) you want to do this as quickly as possible. The longer you drag this out the more painful it will be for you, for her and for your children.
I highly recommend a civil divorce. Be fair, and try to compromise with your ex-wife, rather than fighting. We started out with divorce mediation, but this didn't work for us. I then found a lawyer who specialized in cooperative divorce (after first talking to one who wanted to fight tooth and nail with my ex-wife), and we didn't fight. The result is that now we are civil and cooperate with raising our children... which is a very good thing.
The key to a good divorce is communication. Once I was very clear that I wanted a divorce and that I and wanted to be decent (and not fight), things were easier. The most difficult part of the divorce was when I wasn't sure and was going back and forth... this was painful for both of us. It is the uncertainly that is the worst part, once you make it the divorce certain and let your wife know that it is certain you can both start the grieving process and start to move on.
I hope this is helpful.