The Guide abilities of the alternate Merry and Pippin each refer to the other's alternate version by title ("Meriadoc, Hobbit of the Shire" and "Peregrin, Hobbit of the Shire"), so both Characters must be the alternate versions (and still in the Fellowship) in order to use either's Guide ability. The original versions, "Meriadoc Brandybuck, Hobbit Companion" and "Peregrin Took, Hobbit Companion", don't satisfy the requirement for the alternate versions' abilities.
Oh...you're right. So we've been playing it wrong.
I guess that then changes their usefulness drastically. Losing two Companions due to a hunt tile draw is a bit too drastic, unless a 3 or an Eye (while in Mordor) is drawn.