What if the USSR moved millions of Afghans into Siberia and repopulated Afghanistan with Russians and Central Eurasians?
That would be better than all-out genocide but still have monstrous political setbacks
That's what I was thinking of, although there are two problems:
1. CG's point about the transportation networks into Afghanistan being too limited for large-scale transportation of the unwilling.
2. The Soviets did not intend to annex Afghanistan.
I could imagine the Soviets resorting to something like that out of desperation later on, but such an effort could seriously hurt them.
(Riots among those to be settled in Afghanistan, riots among Afghans resettled in the USSR, an even more savage and desperate resistance movement, the international political repercussions, etc)