A proposal to allow employers to transfer workers with AIDS out of food-handling jobs was killed yesterday by House-Senate conferees even though the provision had been approved by majorities of both houses for inclusion in sweeping legislation to protect the disabled from discrimination.

It is rare for a conference committee to defy majority votes of both houses, and the conferees' action could lead to another row over the food handlers issue when the bill goes back to the House and Senate for final approval, probably later this week.

The legislation, which would guarantee employment, public access and other rights to the disabled, was approved by the Senate last year without the food handlers provision. But after the House voted 199 to 187 to add the provision to its version of the legislation this year, the Senate took the unusual step of voting 53 to 40 to approve a proposal from Sen. Jesse Helms (R-N.C.) to instruct its conferees to go along with the House language.

Such instructions are non-binding, and Senate Labor and Human Resources Committee Chairman Edward M. Kennedy (D-Mass.), a principal backer of the legislation and foe of the food handlers provision, told the conferees that he regarded the Senate vote on the issue as "basically meaningless."

Kennedy asked the House conferees to drop the proposal, and they did by a vote of 12 to 10 over protests from Rep. Steve Bartlett (R-Tex.) that such a move could jeopardize passage of the bill. "We would slow down and perhaps kill the bill for this session if we go against a majority of both houses," Bartlett said.

The conferees' agreement is scheduled to go first to the Senate, where proponents of the food handlers provision could force a vote on the issue. The House could then accept or reject the measure as approved by the Senate.

The provision allows job transfers for food handlers who have communicable diseases, such as AIDS, even if the disease is not transmitted in food, and requires employers to make "reasonable accommodation" for alternative employment.

Proponents of the provision said many restaurants would lose customers and could be forced out of business if AIDS patients cannot be prevented from handling food. Foes such as Sen. Tom Harkin (D-Iowa), chief sponsor of the Senate bill, said it "strikes at the heart and soul of the bill" by "legislating an irrational fear and stereotype."