Yes, counseling will probably do a lot of good.
Even if Dad's visits are supervised now (and even in the short term future), he can petition the court to request regular unsupervised visitation and unless it can be proven that your child IS being harmed (and it will take time to prove this - every child is going to go through a period of adjustment, including anxiety and insecurity, when the absent parent reappears and this is considered a normal process), he will get what he requests.
There are some great co-parenting sites online, and maybe you can take a look at some of them.
You've also really got to get used to the idea that Dad might be around for a long, long time. Any negative feelings you have towards him are going to affect your child and you need to make sure that you're not inadvertently alienating your child from Dad. Because that can actually result in you losing custody.
It happens more often than you may be aware.

