The Spanish full-back left the Reebok Stadium for Fiorentina last summer after opting against a contract extension with the Trotters.
Bolton were able to pick up a compensation fee for his services, but Freedman feels the Championship outfit should never have allowed themselves to be put in such a position.
He told the Bolton News: "It's just another story at this football club. A player is going out of contract and wasn't dealt with in the right way.
"That is exactly the reason why Mark Davies was put on a five-year deal as soon as I got here.
"I know fans want players signed tomorrow and I understand that entirely but you also have to look at the squad and who you are building your team around.
"I was disappointed when he left in the summer but I can't blame the boy for wanting to go and play in Serie A."
Freedman was the man to offer Alonso a regular run in the Bolton team, an opportunity he grabbed with both hands, and the Scot is not surprised to see the 23-year-back in England with a Premier League - having joined Sunderland on loan.
He added: "When I first came here we had Stephen Warnock and I had to look at everyone.
"I decided he (Warnock) had to move on because I had a very good left-back who wasn't even getting a game in Marcos.
"He came in, did great, and we tried to keep him in the end but the lure of Serie A was too good.
"A few months later when he was looking to come back I spoke to Gus Poyet on it and there were a couple of clubs in the Premier League looking to sign him, so I'm not surprised he's doing well for Sunderland."