US based Sovereign Grace Ministries (SGM) has been embroiled in controversy following allegations of a child abuse cover up in its former flagship church; Covenant Life Church (CLC).

Nathaniel Morales, now 56, was convicted on May 15 this year of sexually abusing three underage boys between 1983 and 1991 during his time as youth pastor at Covenant Life. Sovereign Grace is a coalition of 80 Reformed evangelical churches.

During his trial, questions were raised as to whether or not the leadership of the church knew about Morales' transgressions.

In a separate civil lawsuit, bestselling author and lead pastor of CLC during Morales' employment CJ Mahaney (who founded Sovereign Grace) – was accused of being aware of the youth leader's crimes and failing to take action against him.

Mahaney was named as a defendant in a lawsuit which alleged that he and several other leaders of SGM conspired to "permit sexual deviants to have unfettered access to children for purposes of predation and to obstruct justice by covering up ongoing past predation". This case was dropped due to the statute of limitations.

Another former pastor of CLC, Grant Layman, Mahaney's brother-in-law, admitted in court on May 20 that he may have withheld incriminating information about Morales from the police. Layman stepped down from CLC's leadership in March.

Mahaney himself left CLC in 2012 following a leave of absence as a result of allegations from other leaders at SGM who accused him of "expressions of pride, deceit, sinful judgement and hypocrisy". He was later reinstated.

Under the leadership of new pastor Josh Harris – who was accused alongside Mahaney in the civil lawsuit – CLC subsequently left Sovereign Grace Ministries.

Mahaney went on to found Sovereign Grace Church in Louisville, Kentucky which is now the headquarters of SGM.

Controversially, Harris and Mahaney both announced this week that they have left the leadership council of The Gospel Coalition (TGC), described as a "central hub of the Reformed evangelical movement", despite a May 2013 post signed by Don Carson, Kevin DeYoung, and Justin Taylor on the TGC website which defended Mahaney and criticised those who tried to make him "the face of the SGM lawsuit".

Though Mahaney has not offered an official statement on the matter, Harris tweeted on May 19, "I resigned the @TGC Council because I don't want the present challenges at my church to distract from this terrific ministry. Godspeed, TGC!"

"No man can do me a truer kindness in this world than to pray for me. –Charles Spurgeon," he later added.

Tullian Tchividjian, Billy Graham's grandson, has criticised the way SGM have handled the scandal, and said he believes CLC leadership did in fact cover up Morales' crimes.

"CJ was, for many years, the micro-managing head of the organisation and nothing happened under the umbrella of Sovereign Grace that he wasn't made aware of, so for anyone to say, 'Well he didn't know,' that's totally naive," he told the Christian Post.

The fact that Mahaney's brother-in-law has suggested he knew about the abuse, Tchividjian says, further points to the conclusion that Mahaney himself was also aware. "Give me a break. These people, they're family. Of course he knew," he says.

Tchividjian has now also announced his own departure from TGC. In a blog post entitled "I've come to set the captives free", he shares that he has been planning to remove his blog from the TGC website for some time, but was recently asked to do so immediately by the Coalition's leadership.

"In my opinion, the messaging of The Gospel Coalition has morphed over the last seven years and I find myself much more aligned with the very specific message of Liberate [his new ministry]," Tchividjian writes.

"So, now is the right time to pull the trigger. In fact, it's probably overdue."