The felony count carries a potential prison term of up to life, and the lewdness count is punishable by up to a year in jail.
But Judge Glen Dawson instead ordered five years of probation with a year in jail on each count, running consecutively.
Dawson also said the probation was "zero tolerance," meaning that any violation of his probation conditions would land Bothell in prison for the rest of the sentence.
As part of his probation, Bothell must complete sex-offender treatment, must pay $14,000 in restitution and will not be allowed contact with the victims or any other children under 18 except those approved by the Department of Corrections.
Calling it a "very difficult case," Dawson openly struggled over his duty to impose an appropriate sentence.
"These are horrible acts, there's just no two ways to look at that," Dawson said.
Bothell "intentionally or knowingly" exposed his genitals to the same girl and another girl on at least four separate occasions, court documents state.
After being interviewed by police Bothell admitted to touching the genitals of the girl and causing her to touch his penis. He told officers he "accidentally" exposed himself to the same two girls at least eight different times, according to court records.
Bothell's attorney L. Bruce Larsen had argued against prison time, saying his client had been proactive in accepting the consequences since the abuse came to light in August 2012. Bothell admitted his actions to police, voluntarily submitted to counseling and has also paid for the victims' counseling, Larsen said.
"Everything he's done has indicated he is going to change his life," Larsen said.
In a tearful statement to the judge, Bothell said he was remorseful and ready to accept the consequences.
"I'm very grateful that this is moving forward," Bothell said. "I'm grateful that [the victim] saw me lose my job so that she can realize that my employer does not tolerate this kind of behavior."
Dawson questioned Bothell about what led him to "go from family life to these acts," expressing some incredulity that it wasn't somehow rooted in an addiction to pornography, something the judge said he had seen in "99 percent" of the sexual-abuse cases he has seen.
Bothell denied any involvement with pornography but said that he had been exposed to abuse as a young child himself and that his crimes "began with a boundary being crossed."
Prosecutor Cristina Ortega said that while Bothell had been "very proactive" in taking responsibility for his actions, she still pushed for a prison sentence because Bothell's actions were repeated.
"That first incident, there was an awareness that what he did was wrong. And then it didn't stop," Ortega said.
Neither the victim of the sexual abuse nor her father was in court. It was revealed Friday that the victim's mother had died since Bothell was charged. But Bothell's attorney read briefly from a letter written by one of the victims' family members that called Bothell a "wonderful person who did something terrible" and asked that Bothell not be punished by lengthy incarceration.
LDS Church spokesman Scott Trotter said last year in a written statement that Bothell was no longer an employee of the church. Trotter also said that "neither [Bothell's] current or former church positions play any part in this case."
Trotter added: "The Church of Jesus Christ of Latter-day Saints has zero tolerance for abuse of any kind. Those found guilty of these actions are subject to the demands of the law and also face Church discipline. The welfare of victims is our utmost concern and Church leaders will continue to offer counseling and other resources to help in the healing process."
In 2009, Bothell co-authored a magazine article in Meridian, an LDS magazine, on "raising children to feel and recognize the spirit."
He had worked for the church in the Missionary Department at the church office building since 2004 and previously worked as a faculty development coordinator for the Assessment of Student Learning at Brigham Young University, according to his LinkedIn online account. Bothell also has a bachelor's degree and a doctorate in psychology from BYU.