Dear Sir,
Considering the fact that you are residing separately it is better that you go in for a divorce. If possible a mutual consent one if your wife is ready. Further your children are old enough to understand the situation and joint custody of the younger one can be sought for as the child is still a minor. You can continue to maintain them financially.
As for your wife I doubt she will step in for a mutual consent to she already is making allegations against you but still there is no harm in trying considering that you can provide for maintenance and alimony