The term downwell appears to have first appeared in references to things going on inside actual underground wells. This Google N-grams search shows the term coming into use in the late 1950s, and if you follow up the early Google Books links, most of the uses involve "downwell" conditions in oil wells.
Similarly, the Oxford English Dictionary defines the adjective thus: "Located, used, or occurring within the underground shaft of an oil well"; the earliest citation it has is from 1946.
However, the Google Books corpus turns up a clear science fiction usage in the 1987 novel Enigma by Michael P. Kube-McDowell:
"If you clear, I'll okay a pass downwell and a five-day leave so mat you can get your affairs straightened out. Report back on the eighth for orientation. If Tamm can get his people settled, we'll be outbound within sixty days. That's all. You can go.... (p. 39)
This certainly seems to be the same usage seen in other science fiction works (which the OED has not yet documented). Whether this is the earliest appearance of the term is unclear, since the Google Books corpus is by no means complete. It may also have been coined several times independently, by different authors.