She said Zuckerberg also acknowledged the decision had upset many employees and said the company was looking into "non-binary" options beyond either leaving up such posts or taking them down.
One Facebook employee, who tweeted criticism on Monday, posted again on Twitter during the all-hands meeting to express disappointment.
"It's crystal clear today that leadership refuses to stand with us," Facebook employee Brandon Dail wrote on Twitter. Dail's LinkedIn profile describes him as a user interface engineer at Facebook in Seattle.
On Friday, Twitter Inc affixed a warning label to a Trump tweet about widespread protests over the death of a black man in Minnesota that included the phrase "when the looting starts, the shooting starts."
Twitter said the post violated its rules against glorifying violence but was left up as a public interest exception, with reduced options for interactions and distribution.
Facebook declined to act on the same message, and Zuckerberg sought to distance his company from the fight between the president and Twitter. He maintained that while he found Trump's remarks "deeply offensive," they did not violate company policy against incitements to violence.
Twitter last week also put a fact-checking label on two Trump tweets containing misleading claims about mail-in ballots. Facebook, which exempts politicians' posts from its program with third-party fact-checkers, took no action on that post.
Timothy Aveni, a junior software engineer on Facebook's team dedicated to fighting misinformation, announced his resignation in protest over that decision.
"Mark always told us that he would draw the line at speech that calls for violence. He showed us on Friday that this was a lie. Facebook will keep moving the goalposts every time Trump escalates, finding excuse after excuse not to act," he wrote in a Facebook post.
Civil rights leaders who attended an hour-long video call on Monday night with Zuckerberg and other top Facebook executives called the CEO's defense of the hands-off approach to Trump's "incomprehensible."
"He did not demonstrate understanding of historic or modern-day voter suppression and he refuses to acknowledge how Facebook is facilitating Trump's call for violence against protesters," said a joint statement from leaders of The Leadership Conference on Civil and Human Rights, the NAACP Legal Defense and Educational Fund and Color of Change.
Some critics posted calls on Twitter for Facebook's independent oversight board to weigh in. But the board will not review any cases until early fall, and users initially will only be able to appeal to the board about removed content, not content that Facebook has decided to leave untouched. The board, which can overrule Zuckerberg, will only review a small slice of content decisions.
Zuckerberg spoke with Trump on Friday, as first reported by news website Axios.