Wanderers lost an early goal to Andy Keogh's penalty, but they were level by the break as Keith Andrews responded in kind and looked the likelier winners throughout the second half.
It finished 1-1, and Freedman said: "The players showed tremendous effort throughout that performance. That was the most pleasing thing for me.
"If I have any criticisms we were a bit wasteful and our decision making wasn't good enough. Should we have got them towards the end? Possibly through our attacking and opportunities, but it wasn't to be."
Marvin Sordell, who was racially abused by a 13-year-old Millwall fan when the teams met earlier in the season, was jeered by some visiting fans on his second-half introduction.
Freedman said: "I know the Millwall fans and they used to give me a lot of stick. The stick he was getting from them wasn't on my mind when I subbed him on."