Freeney will be back one way or another (they'd use the franchise tag if they had to). It would be better if he was signed long-term in terms of the current cap, and I think that will get done.
June is a big ?. There really aren't that many teams that can really use him because of his small size - so it really depends on what his market value is going to be at.
I expect Rhodes to be signed by another team. I don't think he'll be a starter anywhere, but teams saw how effective having two backs are in the playoffs, so I think someone else will sign him as a change-of-pace back. I think the Colts want to re-sign him, but not for too much $.
I think whether Morris is re-signed will depend on on his market value, too. Two years ago, he was on the FA market and no one else wanted him. He is 32 years old, so I don't think there will be a big market for him.
Harper's a goner IMO. He's up there in years, but good corners (and he's pretty good) get paid, and the Colts can't pay him. I don't know if Jason David is a RFA or a UFA. If he's a RFA, he'll get signed for a 1st round tender (the Colts will likely do the same with their two starting RFA guards, Lilja and Scott).
The Colts will replace Harper with Marlin Jackson, and Kelvin Hayden will become the nickel CB. Freddie Keiaho will likely be a starting LB next year (the Colts really want to get him in the lineup I think) - and he'd replace June if he's gone. If Morris is gone, I'm not sure who would replace him (Tyjuan Hagler? Draft pick? I know it won't be Gilbert Gardner, who's terrible and I expect him to get cut next season). Rhodes will either be replaced by De De Dorsey, the CFL guy they signed, James Mungro, or a 2nd day draft pick.
I really think most of the UFAs will not be re-signed, and it will hurt, but not be a death-blow by any stretch.