The St. Matthias United Methodist Church in Stafford placed 36-year-old Jennifer Brennan on unpaid administrative leave in July after telling authorities they were concerned about her relationship with a 15-year-old boy.
"The congregation as a whole is deeply saddened is just heartsick," said St. Matthias pastor the Rev. Paula Werner.
According to the Free-Lance Star, Brennan counseled the boy, including advising the boy and his girlfriend to avoid premarital sex -- at least with each other. The counseling sessions began to include holding and kissing and eventually sodomy and intercourse.
The alleged incidents began in January and continued through March, the Free-Lance Star reported.
"Over the course of the last six or seven weeks, we have fully and faithfully been a part of this investigation and answered all of their questions," Werner said.
A grand jury indicted Brennan Tuesday on 10 counts each of taking indecent liberties with a child and contributing to the delinquency of a minor.
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Brennan's family and St. Matthias told NBC4 they hope the allegations are untrue.
"Well they've saddened me terribly," Werner said. "My congregation is hurting. All who are involved are hurting over this, and so I am deeply pained by it."