A decision to eliminate a special program at a Ditmas Park elementary school has sparked two weeks of furor among some parents, and struck more than a few commentators as a sign of new mayor Bill de Blasio’s coming war on the gifted and talented.

That rhetoric misses what’s actually happening at P.S. 139, where more than 1,000 elementary school students fill the building that has guarded the corner of Rugby and Cortelyou roads in Ditmas Park since 1902.

For years, that building has been divided into smaller programs, including two “mini-schools” and an advanced program known as Students of Academic Rigor. Principal Mary McDonald’s recent decision to eliminate SOAR for next year’s kindergartners means P.S. 139 is belatedly falling in line with schools in the rest of the city, where most schools’ internal advanced programs disappeared under a Bloomberg administration push to standardize gifted screening — a push driven by equity concerns and led by a top de Blasio education official.

Even though parents know P.S. 139’s SOAR program as a gifted program, it is not a part of the district’s official gifted and talented offerings, which allow students who score high enough on the city’s gifted screening exam to attend gifted programs at six other schools in District 22. Instead, SOAR concentrates many of the school’s highest achievers and allows them to stay together from kindergarten to fifth grade.

“It seems it is a vestige of the old way of doing the gifted programs,” Insideschools’ Pamela Wheaton said. “In pockets around the city, they’re doing their own thing.”

McDonald’s plan, first reported by Ditmas Park Corner last week, will eliminate both SOAR and the mini-schools for incoming students, and teachers will be tasked with providing appropriate work for all of their students.

“We believe we can have both: classrooms characterized by rigor and diversity,” McDonald wrote in a follow-up letter to parents.

The SOAR program admits students based on a test given by the school, and the two mini-schools admit students by lottery. But neither program was open to all in practice, many parents and McDonald admitted. Parents had to request that their child be tested for SOAR and be entered into the lottery for the mini-schools, leaving some less-connected and non-English-speaking parents out of the loop.

Reniya Abdalla, whose daughter attends first grade at P.S. 139, said she saw it happen. She knew to have her daughter tested for SOAR, though she didn’t score high enough to enter the program. But “not everyone knows,” she said.

On Thursday night, McDonald told a group of parents that the school’s current enrollment policies for those programs have created inequity. Both programs have a heavy overrepresentation of students living above the poverty line, a disparity that has been growing each year, she said.

Of the 12 or 13 percent of the school’s current kindergarten class that does not qualify for free or reduced price lunch, just one student is not in one of the school’s special programs, according to McDonald.

McDonald filled a presentation to parents on Thursday with quotes from researchers showing that tracking students by ability level provides negligible academic benefits and significant social drawbacks. “We need to do less assuming that students aren’t aware of the stigma of being placed in ability groups,” she said.

But many parents said they still felt blindsided by the decision, and remain disappointed that students and parents won’t be able to benefit from the smaller communities they formed in the mini-schools and SOAR program. Gela Bulku, whose first-grade son has spent a year in the SOAR program and a year in one of the mini-schools, said teachers in those programs were also more welcoming to parents coming into the school.

“You can go in every day if you want,” she said.

Another parent of a kindergarten student was hesitant about how the changes at the school would affect students and their learning.

“There’s a lot of diversity at this school. That’s a great thing, but do they have a plan for how to mix them all together in one classroom? It’s not a negative, but how do you address that?” she asked.

Department of Education spokesman Harry Hartfield said the decision to eliminate the programs was the principal’s, not the city’s. But changes to the structure of the city’s gifted programs helped pave the way for the school’s current plan.

Almost every school in District 22 had a gifted program before 2008, according to Wheaton. Then, under the leadership of Anna Commitante — who last week was appointed to a top position in de Blasio’s Department of Education — the city standardized the gifted testing process, citing the need to level the playing field across districts.

That change actually made the city’s gifted and talented programs less diverse, with some districts now having no programs at all. It also meant the city decided what schools would have gifted programs, and P.S. 139’s program was eventually phased out.

But officials there continued separating out advanced students on their own, placing them in programs that helped attract students whose parents might have looked elsewhere for a more rigorous curriculum. At P.S. 139 and other schools with similar SOAR programs, the “gifted” label sometimes stuck, even though they included plenty of students who didn’t score in the 90th percentile or above on the city’s gifted and talented test.

“In the neighborhood’s mind, it was 139’s special gifted program,” a mother of a second-grade SOAR student said.

Angelique LeDoux, who runs the organization Parents of Accelerated Learners, said she recognized that the situation at P.S. 139 was not the typical model for gifted education in the city. But advocates of gifted and talented programs will still be watching the school’s future closely, she said.

“What this did when I read about it was raise my eyebrows, and lot of people’s in this space, about what this means for gifted and talented education,” she said.

Those concerned have little to go on, for now. In her first weeks as chancellor, Carmen Fariña has said little about gifted students, though she was a deputy chancellor when the standardized gifted screening was implemented and eliminated the gifted program as principal of P.S. 6 on the Upper East Side. De Blasio has also not emphasized the issue.

Meanwhile, McDonald and the teachers at P.S. 139 will soon have to begin planning for a kindergarten class without internal divisions.

“I think in an ideal world, providing services in heterogenous classrooms and catering instruction to kids’ individual needs would be the best way to do not just gifted education but education at large,” Teachers College professor James Borlan said. “Saying that and actually making that happen are two different things, though.”