OMAHA, Dec. 12— In a city desperate for development, the pricetag on a plan for the new headquarters for a major local corporation is the destruction of a warehouse district that preservationists say is essential to understanding Omaha's role in the growth of the American west.

''The warehouse district, to the best of my knowledge, is certainly one of the Middle West's or the nation's finest collection of this sort of buildings,'' said J. Jackson Walter, president of the National Trust for Historic Preservation.

But to Charles Harper, the chief executive of ConAgra, one of the nation's large agribusiness concerns, the district, Jobbers Canyon, is ''some big, ugly red brick buildings''. He has asked the city to tear them down so his company can relocate its headquarters.

Stretching for six square blocks, the turn-of-the-century brick warehouses loom over a brick street, giving the area its canyon-like effect. Declared Historic District

During the early 20th century, jobbers, or warehousemen, operating out of the buildings, supplied the tools, implements and merchandise for a growing Great Plains region and beyond.

The area was declared a historic district earlier this year. That designation offers protection only if Federal money is involved in the destruction or alteration of buildings.

The struggle to save Jobbers Canyon has pitted Omaha's 500-member Historic Preservation Society against community business leaders who believe locating ConAgra along the riverfront is the key to the downtown's future.

The Omaha Development Foundation, an arm of the Chamber of Commerce, has seized on the ConAgra project as the major investment needed to develop Omaha's dormant waterfront along the Missouri River. A city park would be built as part of the project. A Jan. 4 Deadline

ConAgra's initial project will be $50 million, but city officials say it could eventually reach $100 million and attract $70 million in additional development.

The company has given the development foundation a deadline of Jan. 4 to acquire the riverfront land. If the foundation fails, the company said it would move to another site, most likely in a suburban area.

Omaha's downtown has been steadily losing jobs to suburban office parks. Martin Shukert, the city's planning director, said the importance of keeping downtown healthy outweighed the loss of the historic district. ''This development may not be a large thing to a city with multiple corporate headquarters and a large development industry,'' he said. ''In a relatively small community like this, the effects of a growing, national corporation echo throughout the economy.''

Clark Strickland, director of the National Trust's 10-state regional office in Denver, said the city should not have to make the choice. One of Few Expanding Companies

''To have that area torn down for the necessity of a corporation's image is a very hard thing for a city to do,'' he said. ''It's a shame the city is put in that position.''

ConAgra is one of Omaha's few, expanding companies. It ranks 59th in Fortune magazine's list of the country's 500 largest industrial corporations.

The company is planning a headquarters project that would be a campus-style complex. Critics argue the project is more fitting for a suburban setting and should not be located downtown, particularly at the cost of historic buildings.

They point to the example of Union Pacific Railroad, another major Omaha corporation. The railroad may renovate a 110-year-old freight house close to Jobbers Canyon as its $55 million, nationwide dispatch center.

The Omaha struggle is a front-page story in this month's Preservation News, the National Trust's newspaper, and Mr. Walter has written to Mayor Bernie Simon of Omaha asking the buildings be saved.

''Surely it is not necessary to tear down sound, handsome, historically and economically valuable buildings to create a downtown research campus,'' he wrote.

Mr. Shukert disagrees. ''There is another preservation issue here,'' he said. ''On a metropolitan scale, this project represents the preservation of downtown as a strong, regional center.''