Read OP's post please. They're talking of systems where it was acceptable to always do full table scans, in one case having 350 rows.
Not "an incredibly expensive task on a dataset so big that it needs one". Thus I read OP's post as recommending to not do premature optimization (without using those words literally).
It's something that is likely to require massive engineering effort on a live system.
Removing an index, on the other hand, is never an issue.
It's not at all premature optimization, it's simply basic software design.