Church was designated for assignment by the Braves to clear a spot on the 40-man roster for reliever Rafael Soriano, who made a surprise decision a day earlier to accept salary arbitration.
Instead, Soriano is still with the Braves. The right-hander can't be traded before June 16 without his consent.
The team added about $10 million in payroll with Wagner and Saito, and Soriano could gain a raise from $6.1 million to more than $7 million.
However, despite the Braves' strained budget due to the overstocked bullpen, Atlanta general manager Frank Wren says Soriano's decision will not hinder efforts to improve the team's lineup.
"We knew this was a possibility and was not surprising," Wren told The Associated Press in an e-mail. "It won't change our offseason plans."
Soriano had 27 saves while going 1-6 with a 2.97 ERA in 77 games for Atlanta. Gonzalez, who declined arbitration, had 10 saves.
Church hit .260 with two homers and 18 RBIs in 44 games with the Braves and .280 with two homers and 22 RBIs in 67 games with the Mets, leaving his overall average at .273 with four homers and 40 RBIs.
After batting just .250 with five homers and 35 RBIs for Atlanta, Francoeur produced in New York, hitting .311 with 10 homers and 41 RBIs.
The Church-for-Francoeur trade was one of the few bright spots for the Mets this year.
"I haven't had too many Ws lately, so I'll take it," Mets general manager Omar Minaya said with a laugh at the winter meetings in Indianapolis. "When you haven't had too many, you take anything you can."