I think there are two 'sides' or 'answers' to this.
I think, on the one hand, that it would be best if you separated, especially while they are still young, as it may be easier for them to get used to and they might not be emotionally affected by it in a very severe way if you can still see your children regularly and show them that you and your wife are still friends and get on. Showing them that it's best for everyone will leave them not totally unaffected, but not bitter or angry.
However, I do think that if you do feel that you could 'stick it out' so to speak, for the sake of the children, then maybe you should, but it doesn't sound like you can.
I think that if you do leave, it has to be for good. If you come back, I think that it will only be more confusing for the children and make it all worse.
It's easy for me to say all this, as its not me in the situtation, but I'm just taking my opinions from my own experience of my mum and dad separating - I think it would have been best done when I was young.