Darren Ambrose and Glen Murray's goals sandwiched a Kiko Macheda penalty for United.
Freedman, who has earned plaudits for his work since taking over a cash-strapped club midway through last season, said: "It's a wonderful night for the club, especially given the position we've been in the last few years.
"To play at Old Trafford tonight, we're privileged, the lads learnt a lot from tonight.
"I think we deserved it. We played some stuff, some good football.
"We thought if we came with a gameplan that could be stuck to and everybody played eight, nine, 10 out of 10 we could do it."