The player movement rules were criticised by St Kilda coach Alan Richardson and his Melbourne counterpart Paul Roos on Thursday, with Roos describing free agency as "the greatest de-equalisation policy we've had in the last 100 years of footy".
But Hayes, who spent his whole career at one club, has a different view.
"I think what free agency has done is it's given the players an option, and that's what we wanted," he said.
"I think we should probably reassess it in another three years' time, just to see how clubs are going.
"It think what's hurt (St Kilda) a little bit is the fact that the two new teams came in as we were sort of on a downward slope.
"But that's going to turn around pretty quickly. I'm very confident we'll be up there in the short-term."
"You've got to make the right decisions and get the right people in there to coach them and look after the boys, and I'm really confident St Kilda's got that.
"We're certainly going to be up the ladder before we know it. I think all the Saints fans are looking forward to that, and I certainly am as well.
"So hopefully in a couple of years we'll be poaching a couple of big free agents."
As for whether the Saints should trade the No.1 pick in the upcoming NAB AFL Draft, Hayes said: "I think the number one pick is something pretty coveted.
"We did pretty well last time we had it. We got Nick Riewoldt. If there's another one of him in the draft I'll be very happy."
Hayes added another accolade to his footy resume on Friday afternoon when he was awarded the Madden Medal by the AFL Players' Association.
The medal aims to recognise the retiring player who has contributed the most to the game and the broader community.
Hayes pipped fellow greats like Jonathan Brown, Luke Ball, Nick Maxwell, Dean Cox and Daniel Giansiracusa to win the award.
"It means a great deal," Hayes said after the presentation ceremony in Melbourne.
"The group of retiring players this year have done an enormous amount both on and off the field, and I almost feel a little embarrassed that I've been singled out.
"Any one of those guys could be standing here right now."
Hayes has opted against pursing a career in coaching and will instead concentrate on breaking into the administration side of the game.
He will spend part of next year working at the AFL.
Twitter: @AFL_AdamMcNicol http://afl.to/adammcnicol
