About 3,000 Christians live among 1.5 million Muslims in the Gaza Strip and relations between two communities have generally been good.
"We are one people waging a single struggle for independence and freedom," Haniya, dismissed as prime minister by Mahmoud Abbas, the Palestinian president, after Hamas violently took over Gaza in June, said.
Neighbours said unknown assailants seized Ayyad, 31, on a street near his home in Gaza City late on Saturday. His body was later found elsewhere in the city.
Last phone call
Ayyad's mother, Anisa, said her son had telephoned his family after he was seized.
"He said he was going to be with the 'people' for another two hours and that if he was not back [by then], he would not be returning for a long, long time," she said.
"Rami redeemed Christ with his blood. Rami redeemed the Bible with his blood," she said.
Last April, an explosion at the Holy Bible Society in Gaza City blew out windows and ignited a fire that burned shelves of Christian religious texts and pamphlets. Police said a bomb caused the blast.
Attacks against Christian sites in the territory are rare but at least 40 internet cafes and video cassette shops have been blown up in the past year.