The proximate cause appears to be a falling out over allegations of a sexual abuse coverup, which Tchividjian blogged about publically.
According to Christianity Today, Maheny was accused of covering up sexual abuse, and Tchividjian couldn't associate himself with that.:
Mahaney resigned from The Gospel Coalition (TGC) last weekend in the wake of the criminal conviction of a former youth leader who abused three boys at SGM's flagship, Covenant Life Church (CLC), while Mahaney was lead pastor. On Wednesday, TGC founders Tim Keller and Don Carson gave their explanation of Mahaney's resignation, as well as that of Joshua Harris, CLC's pastor after Mahaney, from TGC's then 50-person council. (They also explained TGC's recent request for Tullian Tchividjian to remove his blog from the Reformed network. Subsequent to the removal request, Tchividjian has publicly criticized how TGC members have responded to the allegations against Mahaney and SGM.)
This position is reflective of the allegations by Coral Ridge Presybterian's pastor, Tullian Tchividijan who is quoted in The Christian Post as writing:
"Give me a break. These people, they're family. Of course he knew," Tchividjian told The Christian Post. "C. J. was, for many years, the micro-managing head of the organization 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."
Furthermore, the same article states as background:
C. J. Mahaney, who founded the SGM, along with other ministry leaders, was hit with a civil lawsuit last year alleging that they 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."
While the lawsuit was thrown out due to statute of limitations, Tchividjian said that unlike many of those connected to TGC who considered Mahaney a friend and claimed that he had "been the object of libel and even a Javert-like obsession by some," he saw the situation differently. In his eyes, given that Mahaney's brother-in-law and fellow former pastor at Covenant Life Church had confessed to knowing about sex abuse claims and withholding that information from police last week, the SGM pastor was guilty.
There is a longer interview here.
For his part, Mahaney denies the claims, saying:
"I look forward to the day when I can speak freely," said Mahaney. "For now, the simple and extraordinarily unsatisfying reality—for myself and others—is that in the face of an ongoing civil lawsuit, I simply cannot speak publicly to the specifics of these events.
"Even with those constraints, however, let me be clear about this: I have never conspired to protect a child predator," Mahaney continued, "and I also deny all the claims made against me in the civil suit."
There does appear to be reconciliation, however - From this article in Christianity Today:
Tchividjian also affirmed his friendship with TGC co-founder Tim Keller, and emphasized that TGC and his Liberate ministry are "on the same team" because "the harvest is ripe enough for well-meaning brothers and sisters to agree to disagree."
Meanwhile, Russell Moore wrote that he is more in agreement with TGC than Tchividjian on the sanctification debate, but the Ethics and Religious Liberty Commission president praised the apology as "something we all can learn from, and ought to reflect on."
He also compared it to how conservative Christians received World Vision's apology for attempting to hire gay Christians in legal same-sex marriages. "Our attitude should have been, from the beginning, to show faith working itself out in love," wrote Moore. "That means believing the best about another, unless proven otherwise."
This entry mentions that there are differences in regards law and grace - and that there are accusations of Maheny using grace to cover for sin. That may be the doctrinal differences being talked about, but let's face it: even if the doctrinal differences are about the degree to which a pastor should exercise grace or justice when dealing with accusations of child abuse, the truth is, even as the announcement says, "the matters are pastoral"