I found a solution to this in the post "Sorting threads after gathering
threads" [1], and some bug reports [2] [3]. I used the patch in [2]
against gnus-sum.el, placing the relevant parts into a function that I
call from my gnus init file. I've attached the function here, and that
along with something like:

    (load "~/.emacs.d/gnus/gathered-threads-by-subject-sort.el")

is the *only* way I've found to get the sorting order I want when
gathering threads by subject in Gnus -- sorting the most recent threads
towards the bottom with sorting done by the most recent message rather
than the root/oldest message of threads.

[1] http://emacs.1067599.n8.nabble.com/bug-21462-25-0-50-Gnus-thread-gathering-and-sorting-inverted-td368462.html
[2] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=18156
[3] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=21462