Incredibly difficult question, and one to which I would normally answer "irrelevant" - but voting for Craig Cumming as better than both would be something of an insult.
Should've picked, I dunno, Arthur Morris or Geoffrey Boycott.
Both excellent openers who remained excellent despite technical flaws which sometimes caused repeated dismissals, because they were good enough to work at making these flaws less of a weakness. How many times around 1997-1998-1999 sort of time did we see Kirsten get out dragging onto his stumps? But he worked hard and cured the problem.
Atherton certainly looked the more natural batsman, but it was Kirsten who certainly did more by the close of his career. This can be explained in a fair few ways - Kirsten never suffered the condition Atherton did; this meant not only did he have no bouts of unavailability or affected performance, but he could go on longer than Atherton and have a short spell at the end of his career where he cashed-in a bit on the degenerating quality of bowling and flatness of pitch.
All told, I'd probably vote for Kirsten because although I don't think he was neccessarily the
better batsman, he had less misfortune so was therefore marginally the more effective.