The solution to your problem lies in this statement: "She filed a counter reply stating the she now wants to live with me."
Your advocate is right in saying that you will NOT get divorce based upon cruelty. She will have her own version and as you have a child and she is willing to come back to you, there is no way you will be able to claim cruelty and get divorce from her on grounds of cruelty. In general, cruelty as a ground for divorce initiated by husband is rarely granted. Exceptional cases could be false cases filed by you or your parents which resulted in imprisonment or some such extreme cases where evidence is right there... falsified claims resulting in imprisonment. In your case, it is your word against her. She can claim that you suggested the name of your girl and that she repeatedly begged you to take her and the child back but you refused... Get it?
What I suggest is that you take a practical approach giving highest priority to the interest of the baby. Consent to her willingness to come and stay with you. In fact, file a RCR or some such application yourself in response to her reply stating that she is willing to come and stay with you. Just check. May be her intents are genuine. Get a Court Order to that effect that you are and always were wiling to let her stay with you.
If she does NOT decide to come and stay with you, then and only then, you file a new petition, this time seeking divorce based upon desertion by her. It will be easy for you to get it because you will be able to prove that indeed she has deserted you. Mere separation for more than two years does not suffice to seek divorce based upon desertion. For example, she can claim that you made it impossible to stay with you. Her willingness to come back to stay with you now will blunt and condone forever any defenses/allegations by her or you in the future on the basis of cruelty. That is the key to getting divorce based upon desertion by you in the future. If she had bad intentions and is crooked, she can come for one month and then leave again... that could upset your strategy because desertion period has to be continuous. But you can argue that she came precisely for that... to blunt your desertion argument. I am not too sure if that argument will fly... it gets complicated. Visit that scenario when it comes to that.
So.. to conclude... allow her through a Court Order to come back and stay with you. If she comes, do compromise on a few things in the interest of your child, and forget about divorce and the past. Try your best to work things out when you are together with her. If not, well, you know it was a trick by her but the trick would have turned against her. Your desertion argument will become solid. File a fresh petition for divorce based upon desertion. If you refuse in Court to let her come back, it would be a legal blunder and a moral mistake too in case her intents are genuine.
Also, remember that a wife who refuses to live with her husband (unless it is proven by her that it is impossible to live with him) loses her right to maintenance. So, there are many reasons for you to consent to her request to come and live with you.