It seems like a strange decision given that Khomeini was initially imprisoned, and then exiled, which allowed him to continue preaching to his followers from Iraq and later France.
Khomeini had a great deal of prestige as a religious leader. As well as being an ayatollah he was also a marja - a person acclaimed by many other clerics as being worthy of emulation. If I have understood right, such a person is sacrosanct, and so killing him would have led to huge protests.
Source - Revolutionary Iran by Michael Axworthy