I see 2 issues here (and I agree it is annoying):
1) Really annoying is the loss of place in the list, when the screen jumps to line 1.
It would be nice if Calibre could remember the current "Line" number in the view
2) Suspend the Resort on rename and simply require the user to trigger a manual Sort.
The record does not automatically seek (Fly away) to it's new location
Note: Adding new books leaves the new books at the Top (Line 1 to x) until something else triggers the sort. That would work.

A "Suspend Sort" (leaves the order, just as it is) button that inhibits resorts while depressed (colored when pressed to remind us)