The June 25 letter to Obama, coauthored by representatives of more than 100 religious-based groups, states: "As you seek to promote the rights of LGBT persons, please also protect the rights of faith-based organizations that simply desire to utilize staffing practices consistent with their deep religious convictions as they partner with the federal government via contracting or subcontracting."
Obama on Monday signed an order prohibiting federal contractors from discriminating in hiring on the basis of sexual orientation, with no exemption for religious groups.
Ryan Paetzold, a 2007 Eastern graduate and director of the alumni group OneEastern, said nearly 800 people had signed a letter to Duffett asking him to withdraw his signature.
"We were really shocked by this," Paetzold said.
He questioned Duffett's argument about the separation of church and state.
"We're confused," he said. "We don't believe the right to discriminate has any bearing on that."
Paetzold also questioned Duffett's assertion that Eastern does not discriminate when its faculty handbook states employees can be terminated for "moral turpitude," of which homosexual conduct is listed as an example.
"What's the correlation for students?" asked Paetzold, a Lutheran pastoral candidate from Marlton. "We just want it to be a safe place for students."
Duffett said in an interview that the policy is not discriminatory because it also prohibits heterosexual sex outside of marriage.
"We're trying to be evenhanded on that," he said.
He said he was not aware of any employees who have been terminated for either reason.
The issue at Eastern, Duffett said, is emblematic of a larger conflict facing the country: "We're really talking about, how do we have freedom of faith and on the other hand the embracing of all people?"
Eastern, he said, welcomes all students, including LGBT students. Paetzold said the university has a long way to go.
Paetzold, who graduated from Eastern with a degree in biblical studies and youth ministry, attended Eastern's seminary after graduation but transferred to the Lutheran Theological Seminary in Mount Airy, which he said he found more "welcoming and affirming" to LGBT students. An LGBT student group only recently was given club status at Eastern, he added.
The alumni group wants Eastern to adopt a stronger antidiscrimination policy for students and staff that would protect lesbian, gay, bisexual, and transgender students.
About two dozen leaders of other religious-based colleges around the country also signed the letter to President Obama, including Geneva College in western Pennsylvania, College of the Ozarks in Missouri, and Colorado Christian University. Eastern is affiliated with the American Baptist Churches USA.
The president of Gordon College, a small Christian school in Massachusetts, signed an earlier letter - it was the lone college to be a signatory at the time - and has faced a backlash from some alumni and a review by a regional accrediting agency as a result, according to published reports.