"I am looking at our donors now...what they will say about the pardon," said Mutharika.
The president came under fire from donors for oppressing the rights of minorities. More than half of Malawi's development budget comes from foreign donors.
"Is it possible to stop aid to Malawi because of two people who are insane?" he said.
Mutharika pardoned the two men, who held a wedding ceremony in December, after meeting last month with UN Secretary-General Ban Ki-moon.
The general public in Malawi had been supportive of the tough sentence against the men.
"The story ends there...I don't want to hear anyone commenting on them. Nobody is authorised to comment on the gays. you will spoil things," Mutharika told reporters when he arrived after the Africa-France summit in Nice.
Although the couple has been pardoned, rights group Amnesty International is warning that they could face further harassment unless the law is changed.
The men said they were beaten by police while in custody.
"Malawi must live up to its obligations under international human rights law," said Michelle Kagari of Amnesty. "The authorities are legally bound by these treaties to take effective steps to prevent acts of violence or discrimination and to privacy, without discrimination on the grounds of real or perceived sexual orientation or gender identity," she added.