PBS also sued the government about the EO. Not just NPR. It wasn't unilateral. Here's NYT reporting on the PBS lawsuit.
They needed to be a party to the lawsuit, but compromise was their first choice. Again, I reference the December NYT article, which suggests it was Maher that didn't want to compromise, even when it might have been possible after the lawsuits were filed:
In April, as Congress was gearing up to claw back funding from the public media system, America’s Public Television Stations, an influential nonprofit advocacy group, sent a document to leaders of NPR, PBS and the Corporation for Public Broadcasting.
The document listed several scenarios that might allow NPR and PBS to save funding for local stations by agreeing to give up money for national programs. It even included a “save-face rationale” for some Republicans in Congress who wanted to justify their support of public media.
....
At a meeting soon after, Ms. Kerger and Ms. Maher expressed support for such a compromise. It seemed, briefly, like the heaviest hitters in public broadcasting were on board with the plan.
But there were also signs of major strain.
On a call this spring, Patricia Harrison, the chief executive of the Corporation for Public Broadcasting, asked Ms. Maher whether she would be willing to say anything to members of Congress or the press to acknowledge concerns from listeners who viewed NPR’s reporting as biased, according to two people familiar with her remarks.
Ms. Maher rebuffed that suggestion. She didn’t believe that NPR was biased, and she thought saying so would undermine the organization and fail to placate those who were critical of the network, according to a person familiar with her thinking. After she refused, months of simmering tension between the Corporation for Public Broadcasting and NPR came to the surface. Ms. Harrison told Ms. Maher she should resign her position for the good of public media.
Things got more tense when, on May 1, Mr. Trump issued an executive order banning government funding of NPR and PBS. NPR sued the White House, arguing that the order violated the Constitution. And it added the Corporation for Public Broadcasting as a defendant, since Mr. Trump’s order directed it to deny NPR funding.
NPR also changed its position on the funding compromise: It now viewed any cuts as a violation of the First Amendment, essentially arguing that cuts amounted to government discrimination against NPR based on its viewpoint.
Ms. Maher said that once the Trump administration attempted to tie the organization’s ability to receive federal funding to its editorial decisions, the compromise “was no longer an option.”