Attempts to obtain the cooperation of Saw Gerrera on Jedha have been ended at the recommendation of General Jan Dodonna.
[Document #NI3814 (“Situational Analysis Regarding Jedha, et al.”), timestamped approximately thirteen years after the conscription of Galen Erso by Orson Krennic; from the personal files of Mon Mothma.]
Rogue One official novelization by Alexander Freed, Prologue

Why did General Dodonna recommend to end trying to cooperate with Saw Gerrera?

  • Are you looking for a specific incident? "“Yes, but Saw Gerrera’s an extremist. He’s been fighting his own war for quite some time,” Mothma said. “We have no choice but to try to mend that broken trust.”" – Valorum Dec 18 '16 at 19:14

The Rogue One: Rebel Dossier factbook contains an in-universe briefing file on Saw Gerrera. In short, his violent anti-Empire methods don't align with the touchie-feely 'winning hearts and minds' campaign that Mon Mothma considers to be the best way of defeating the Empire.

He's evidently prone to acts of aggression that disrupt the lives of ordinary citizens and give the Rebellion a bad reputation as 'anarchist terrorists' rather than 'freedom fighters'. A case in point is the attack on the Imperial forces in Jedha, undertaken in full view of the citizenry with zero interest in their safety.

His years of fighting the Empire have left him unstable, so consumed with hatred for the Empire that he has done more damage than good to the rebel cause. Since retreating to Jedha, Gerrera has done our movement relatively little harm.

But I fear what he will do when he receives Erso’s message. He is likely to foolishly lash out, as he has done ever since his days as a young resistance fighter on Onderon.

Saw Gerrera’s fatal flaw as a leader is he’s never understood that most people value peace and order even more than freedom. Our rebel cause gains support when people believe we can make them safe and free from the Empire’s tyranny. It loses support when people believe we will replace the Empire’s order with chaos and danger.

Rogue One: Rebel Dossier

There's also some info in the Star Wars: The Rebel Files factbook about the reasons the Rebel Alliance distanced itself from him and a 'notice of censure'. In short his actions were "morally repugnant" in targeting civilians and innocents and employing torture in interrogation.

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Probably disagreements about strategy

The novelization implies that Dodonna preferred low-profile "covert strikes," seeking to avoid the Empire’s gaze:

As an organization, the Rebel Alliance was held together more by external pressure than by internal bonds. Mon Mothma’s almost pathological need to make political overtures toward peace—regardless of their success—was a poor match for General Jan Dodonna’s policy of covert strikes that minimized attention from the Empire and its Senate. Dodonna’s approach, in turn, was incompatible with Bail Organa’s desire to rapidly intervene wherever Imperial atrocities occurred. Saw Gerrera had effectively withdrawn from the Alliance over strategic disagreements; but there were other council members who shared his more aggressive agenda. If not for the Empire’s overwhelming strength—if not for the need for the rebels to work together to even survive—the Alliance would have fractured in a matter of months.

Rogue One: A Star Wars Story

This would stand in marked contrast to Gerrera’s preference for more direct action, which certainly attracted the attention of the Empire:

These were not the rebels Galen Erso had described: gallant men and women whose righteous hearts led them to oppose the horrors Bodhi had seen, the deeds in which he’d been complicit. Instead, these were the rebels the Empire had always warned of: the murderers, the criminals and terrorists who concealed their viciousness in a patriotic wrapping. The ones who saw the deaths involved in spaceport bombings as a small cost for smaller victories.

Rogue One: A Star Wars Story

While there may have been a specific event that motivated their disagreement, this is not known as of yet. Saw Gerrera is slated to appear on Star Wars: Rebels, though, so we may get some additional information on why he departed, and perhaps Dodonna’s role therein.

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