The army said the destruction of the homes had been postponed pending an appeal of the action by the two men, who are in Israeli custody.
Kuntar and four other prisoners being released as part of the deal are the last of the Lebanese prisoners in Israeli custody.
He also went to Israel to make sure independent autopsies were carried out on Palestinians who died in Israeli custody.
Henning Mankell is taken into Israeli custody after an attack on a Gaza flotilla.
The demands apparently include the release of the most prominent Palestinian leader in Israeli custody, Marwan Barghouti.
About 7,000 Palestinians are in Israeli custody.
The Red Cross discovered them in Israeli custody in January 1992 and informed their families.
The center also said two other members of the Abu Hein family remained in Israeli custody.
A spokesman said a member of the Gaza staff had been in detention for two years, but knew of no one else in Israeli custody.
As of 11 July, 38 detainees had been deported, leaving 82 still in Israeli custody.