Your question is worded so strange. You don't say you want to leave your husband, you say your counselor tells you to. Are you ashamed to say you want to leave him? Do you feel like you'll be judged - so it looks better if an official with training has told you to? Or are you not sure you want to leave?
I divorced my first husband. I am not against divorce or one of the types that will tell you the evils of divorce. I just wonder why you say it like that. If you DON'T want to leave him -- change counselors. Look into couples therapy. See if you can save your marriage. Make sure when you do leave him it's because YOU want to. Not because someone told you to. This is your life.
Now, as to the kids. If the divorce is your choice, and your husband is abusive, hurtful, controlling, neglecting, alcoholic/user or some other serious offense -- you're helping your kids as well. Yes, you will lose some time -- but you can make the most of the time you do have, and you will know that you're not raising you children in a toxic environment. Remind yourself that being a parent is making the best choices you can for yourself, and your kids. Like they say, the right choices are often not the easy choices.
Good luck to you,
H.