The expression, "So it goes," was a standard one well before the 1960s dates of either of the science fiction works you mention. Although Google Ngrams results must be taken with a grain of salt (the makeup of the corpus is not consistent over time, and many scanned documents are misdated), a simple search indicates that the popularity of "so it goes" may have peaked in the 1940s.
Ellison's usage just seems to be everyday use of a normal idiomatic expression. On the other hand, Vonnegut uses, "So it goes," as repeated motif in Slaughterhouse Five; the quote is repeated after each death that occurs in the story. So, to the extent that the phrase is widely recognized in science fiction, that is probably Vonnegut's influence.