Usage of "intern" in this sense is much older than Common Lisp. The earliest reference I could find in a few minutes of searching is from 1974, from the MACLISP Reference Manual:

http://www.softwarepreservation.org/projects/LISP/MIT/Moon-M...

See sections 6.3 and 6.4 and the glossary for definitions and uses of the word.

Unfortunately they don't shed any light on where the term "intern" comes from. Typical usage is that a string is «"interned" or registered in an obarray» but it doesn't explain much more than that. Interning occurs most often at read time, when a string read from the input is turned into an atom, so I'd guess that "intern" is short for "internalize" or similar.