If my wife and I are separated and in the process of divorce, can she changed my daughter's last name without my permission?

Unfortunately--there is not much you can do about it.  There are automatic temporary restraining orders (ATROS) included in the summons for dissolution.  However, those ATROS do not restrain the parties from changing the child's name.  I understand that this is upsetting, but accept it and move on. 

You should really hire an attorney to assist you in this process and ensure you get the best outcome possible.

Best of luck.