Because not everyone was executed in the Soviet Union. Khrushchev was politically harmless and, therefore, pointless to kill in 1964.

By 1964, Khrushchev's power within the government declined significantly. Most people, even those who personally owed their job to Khrushchev, no longer supported him. The coup was more or less an open secret in the halls of the Soviet government. Khrushchev simply refused to believe it could actually remove him from power. Until it did.

Khrushchev had no fight in him when he realized he was being removed from power. The night after he was informed of being removed he phoned Anastas Mikoyan and said this:

"I'm old and tired. Let them cope by themselves. I've done the main thing. Relations among us, the style of leadership, has changed drastically. Could anyone have dreamt of telling Stalin that he didn't suit us any more, and suggesting that he retire? Not even a wet spot would have remained where we had been standing. Now everything is different. The fear's gone. That's my contribution. I won't put up a fight."

Since Khrushchev was clearly demotivated by the coup, there was no point in executing him. He had no respect left among the people, no support in the Party. Although some of his approach in government resembled Stalin, at this point in his life he clearly wasn't a ruthless leader anymore.

Even during his best times, he was sort of a grandpa. A bit fat, short, loud and funny in a cute way. After all, his upbringing ensured that he was a normal dude, so he liked to joke around and keep a friendly demeanor. And although he was clever and tough, nobody feared him like people feared Stalin. That's why Khrushchev had two coups against him, the second of which removed him from power.

Those who planned the coup didn't even want to make it seem like one. Vladimir Semichastny, the KGB chief, said this about the meetings during which Khrushchev was told of his removal:

"I didn't even close the Kremlin to visitors. People were strolling around outside, while ... in the room the Presidium was meeting. I deployed my men around the Kremlin. Everything that was necessary was done. Brezhnev and Shelepin were nervous. I told them: 'Let's not do anything that isn't necessary. Let's not create the appearance of a coup.'"

Barely anybody visited Khrushchev during his retirement. When he died in 1971, few mourned his passing. The official communist newspaper, Pravda, only published a short blurb about his death. The single matter-of-fact sentence was a symbol of how much his status diminished in the seven years since the Brezhnev coup. Often leaders end up with libraries named after them, whole institutions, even cities if they're deemed great enough. Khrushchev? Well, his hometown has a couple of streets named after him. That's it.

Source:

The Khrushchev Era 1953-1964 by Martin McCauley.

A Russian documentary film: Khrushchev. First After Stalin. https://www.youtube.com/watch?v=SvebBtXFxLE&t=8s