A well-known Israeli Army colonel has resigned as commander of a combat brigade in Lebanon, asserting that "his conscience and his outlook did not permit him to continue taking part in that operation," Israeli military officials said last night.

The announcement did not identify the officer, but military sources today confirmed reports that he is Col. Eli Geva, a 14-year veteran from a family with deep roots in the Israeli military.

The resignation of a combat commander during wartime to protest government policy was thought to be a first in Israel's conflict-filled, 34-year history. It also was another sign that doubts about the human and political costs of a military strike into Beirut are beginning to surface as the Israeli invasion of Lebanon passed the 50-day mark.

Initially there was almost universal support here for the announced objective of the military operation, which was to clear the PLO from a 25-mile corridor in southern Lebanon along Israel's northern border. Even when Israeli troops moved far beyond the 25-mile goal there was little public dissent because of the swiftness and the success of the advance.

When Israeli forces trapped the PLO inside West Beirut and negotiations over removing them began to drag on, however, the first signs of opposition began to emerge. Muted over the past three or four weeks, foes of the government of Prime Minister Menachem Begin have again begun to express their doubts about current policy, although Begin still appears to enjoy overwhelming backing within the country and retains full freedom for maneuver.

Geva, 32, was described as a "dove" on the question of Arab-Israeli relations but also as a highly respected officer. During the 1973 Arab-Israeli war, he led troops against the Syrians in the Golan Heights, where some of the bitterest fighting of that conflict took place. Geva's father was a major general in the Army, the highest rank short of chief of staff. One of his brothers, also an officer, was blinded during the fighting in the Golan Heights in 1973.

In the mid-1960s Geva's father, Yosef, was a military attache at the Israeli Embassy in Washington where Eli Geva attended high school.

One measure of the esteem for Geva within the military were reports that Begin, Defense Minister Ariel Sharon and Chief of Staff Rafael Eitan all tried personally to dissuade him from resigning.

Although there was no official confirmation, Geva's role in the current invasion of Lebanon was said to include spearheading the Israeli assault on the Lebanese coastal city of Tyre. He then led his troops to the outskirts of Beirut, where with other elements of the Israeli Army he has been awaiting the outcome of the protracted negotiations over the fate of the Palestine Liberation Organization forces trapped in the city.

Neither the military announcement nor press reports elaborated on the reasons for Geva's decision. But military sources said that his "conscience problem apparently relates to joining a battle for Beirut because of the large number of civilian casualties" that could be expected and the losses the Israeli Army is likely to take.

In that case Geva, although still clearly in a minority, is not alone among Israelis as they consider what next to do about the trapped PLO forces in Beirut and the situation in which their country finds itself throughout southern Lebanon.

Today Shimon Peres, the leader of the opposition Labor Party, called a news conference at which he reiterated his party's objections to a military attack on West Beirut. Peres said he believed a political solution to the siege of Beirut was possible and he suggested that the government should be more "flexible" in demands, for example by agreeing to an interim solution that would allow the PLO fighters to go first to Tripoli in the north of Lebanon and to the Bekaa Valley.

Only last week Defense Minister Ariel Sharon rejected suggestions of such an interim plan that surfaced following President Reagan's meeting in Washington with the foreign ministers of Syria and Saudi Arabia.

Peres' comments were similar to those made by former Israeli prime minister Yitzhak Rabin in a television interview Saturday night. Peres and Rabin are rivals within the Labor Party, and there were undoubtedly elements of political maneuvering in their statements. Nevertheless, the questioning of what, after seven weeks of war and more than 300 deaths in the battlefield, Israel can still hope to accomplish in Lebanon and at what further cost is not confined to the politicians.

Yesterday Jerusalem police broke up a demonstration near Begin's office by 15 opponents of the war. Israel's small Peace Now organization and a group calling itself The Committee of Arab Citizens Against the War in Lebanon have scheduled news conferences this week to press their demands for an end to the Lebanon crisis.

Meanwhile, the Israeli press is carrying increasing amounts of commentary questioning whether the Begin government can achieve its announced goals without a bloody battle on the streets of Beirut.

So far the Israeli government has given no public indication that it is ready to consider backing off its commitment to eradicate the PLO from all of Lebanon, even if that requires exercising what is called "the military option." But there are also reports that the questioning has now spread to the Begin Cabinet.

The Jerusalem Post last week quoted an anonymous "senior minister" as saying that the Cabinet is badly split over the question of attacking West Beirut directly and was growing impatient over the continued deadlock in the negotiations being led by U.S. special Middle East envoy Philip C. Habib.

"There is a strong feeling in the Cabinet that the time has come to end the affair," the minister was quoted as saying.