Auto-collections do not touch database, they are pseudo-collections created on the fly, the same way as purchased content or unread books are - you do not have to disable anything, there is no penalty on the system whatsoever. Simply do not use them - that's all.
Or stop using Calibre
Or reconfigure Calibre to your liking. Or think of something else: I do not use Calibre, but software I am using also creates directory per author - and then some - like series. And I am using my auto-colections almost exclusively, by additionally grouping books (business, trash, e.t.c.). You see auto-callections still support searching and sorting...