Correct! Protecting farmers has no sense in the base game, but some expansions may turn it valid option.
Protecting farmers just in case there is a meeple exchange would be similar to placing a wagon on a German castle and protect it. The only thing you are doing is being extremely cautious or revealing your intentions beforehand. You can always delay the meeple protection, but you won't have this benefit if you are not the active player. So it is up to you to decide.