March 27, 2014 -- Teachers at Timberlake Christian Schools started asking Doris Thompson whether her granddaughter was a lesbian shortly after the little girl chopped off her waist-length hair to donate it to cancer patients, Thompson said.

Sunnie Kahle was only 3 at the time.

Now that Sunnie is 8 and in the second-grade, a Virginia school has said it will not allow her to return in the fall "unless Sunnie as well as her family clearly understand that God has made her female and her dress and behavior need to follow suit with her God-ordained identity."

“When I got the letter, I was just sick,” Thompson told ABCNews.com. “She’s a little tomboy, so I let her be what she wanted to be.”

Last month, Thompson said, school principal Becky Bowman sent her a letter asking that she not re-enroll Sunnie at Timberlake Christian Schools in Forest, Va., because students weren’t sure whether she was a boy or a girl.

“You’re probably aware that Timberlake Christian Schools is a religious, Bible-believing institution providing education in a distinctly Christian environment, and we believe that our biblical role is to work in conjunction with the home to mold students to be ‘Christlike,’” Bowman’s letter reads, elaborating that her school “reserves the right” to refuse admission to students on grounds of homosexuality or alternative gender identity. “It seems that the school’s goals and biblical foundations are going to be in contradiction with the direction that Sunnie is heading at this point.”

Bowman declined to comment, directing ABCNews.com to the school’s lawyers at Liberty Counsel, an Orlando, Fla.-based nonprofit that provides pro bono assistance “dedicated to advancing religious freedom, the sanctity of life, and the family since 1989.”

“The little girl has never been accused of being a lesbian or transgender,” attorney Matthew Staver, founder and chairman of Liberty Counsel, told ABCNews.com.

After being read the letter that Bowman wrote to Thompson, Staver said Sunnie wasn’t denied re-enrollment because she behaved like a boy. He said the issue was more about “what the [grandparents] are doing,” declining to elaborate.

Thompson, whom the school recognizes as Sunnie’s legal guardian, has not filed suit against the school.

Thompson, who’s raising the girl with her husband, said she put Sunnie in Timberlake because she wanted her to get a religious education. Since receiving the letter, however, Thompson has moved Sunnie to public school. Although Sunnie misses her friends at Timberlake, she told Thompson she was bullied more by the teachers than the students, Thompson said.

Although Bowman wrote in the letter that Sunnie seemed to be having gender-identity issues, Thompson said Sunnie always says she’s a girl, though she happens to like collecting baseball cards and rocks, and practicing using her BB gun with her grandfather.

Sunnie, whose mother is unable to raise her, has short hair, and preferred to wear khaki slacks with her Timberlake uniform instead of a skirt, something many of the other girls did, too, Thompson said. “I guess it was her hair,” Thompson said. “I don’t know.”

Sunnie’s pediatrician has repeatedly told Thompson not to even think about her sexual orientation until Sunnie reaches puberty. When she told a Timberlake teacher that, the teacher told her, “You need to find a Christian doctor,” Thompson said.

But if Sunnie decides she’s attracted to women when she’s a teenager, Thompson said, “I’ll love her more.”

“She is very headstrong. She has a heart of gold,” Thompson said. “She knows what she wants, and I hope that will continue with her throughout her life.”