President Carter is now putting finishing touches on an executive order designed at last to charter a future course for the beleaguered Central Intelligence Agency and end its vulnerability as Congress's favorite whipping post.

But the four-year victimization of the CIA has left deep wounds that the President's new charter can do little to cure. Indeed, even as Carter prepares to sign - perhaps this week - the executive order restyling the CIA, Adm. Stansfield Turner, CIA director and principal draftsman of the executive order, continues to alarm professional intelligence officers with sometimes heavy-handed internal reforms.

Chief of these is Turner's plan to fire some 800 senior intelligence officers out of a total 4,500, which he privately announced to top CIA staffers last month without elaboration or explanation. To some intelligence experts, both in the United States and among allied nations, the firings between now and Oct. 1, 1978, will create a pool of virtually unemployable, middle-aged intelligence agents, some of whom might be ripe for going public with intelligence secrets (as many other ex-CIA agents have recently done) - or even for recruitment by the Soviet KGB.

A remarkably similar situation occured following the bloody, post-Stalin political upheaval in the KGB in 1953, which produced an invaluable intelligence haul for the United States. This was directly traceable to a sense of betrayal among ousted KGB agents.

The Carter-Turner CIA reorganization has been drafted with scrupulous attention to legal detail so that the executive order can stand on its own without an immediate new congressional law (whcih can'be passed until next year). Accordingly, Turner's title will not be elevated to Director of National Intelligence, as originally planned. He remains Director of Central Intelligence with overall supervision of the government's ramified intelligence units, but with no day-to-day control over the operations of the Pentagon's National Reconnaissance Office, which controls U.S. satellite spies; the National Security Agency, responsible for communications intercepts, among other duties; and the Defense Intelligence Agency, with its Army, Navy and Air Force components.

In return for losing out in the bitterly contested power struggle over direct supervision of these peripheral but vital units, Turner will wield general budget control over all intelligence agencies and will be given new "tasking" powers to decide which one should perform different intelligence gathering tasks.

In addition to the new National Tasking Center, to be headed by a Turner aide with Turner as chairman of a National Security Council committee with ultimate tasking authority, the executive order will also consolidate all intelligence analysis under Robert Bowie. He will head an office to be called the National Foreign Assessment Center.

Bowie is an experienced expert who headed the State Department's Policy Planning Staff under John Foster Dulles. He was brought into the CIA early this year from Harvard and in this nes role must tap assessments and analyses from all intelligence units in the government. Presumably, Bowie will be responsible for the daily intelligence briefing given to the President.

That leaves human (as opposed to scientific) intelligence-gathering and secret or clandestine operations abroad - the source of the CIA's problem with Congress. Sen. Frank Church, chairman of the committee that investigated the CIA in 1975 and 1979, is insisting that the CIA's new charter spell out precise limitations on the CIA's secret operations, including a specific veto on "conspiring to overthrow democratic governments." He wants these prohibitions repeated in the new law, a demand that both mystifies and angers some other senators.

"So we spell out no overthrow of democratic governments," one senator told us. "Does that mean full speed ahead in non-democratic countries?"

The President's executive order is expected to define broad procedures governing CIA dirty tricks, leaving specific prohibitiobs to congressional over-sight committees, which must be informed on all clandestine operations.

Experienced intelligence men, however, fear that the question of foreign operations may be moot in Turner's CIA, no matter what the new charter says. "He's a nut on the scientific gimmicks," one told us, "but doesn't put much stock in human-source intelligence or dirty tricks."

If so, the new CIA will start out hobbled in the always dangerous competition with the far-flung KGB.