Indeed. I can think of a couple of other creatures who are definitively described as having "good" or "evil" natures that are in opposition to their otherwise explicit "Chaotic" or "Lawful" alignments (respectively). The Horde, Hydrax, and Undine all fall into the category of having Good/Evil intentions that belie their Lawful/Chaotic alignments.
For a BECMI style Dragonlance campaign, I imagine you would want to define whether the ultimate conflict is supposed to be one of Good vs. Evil (like in the books) or something else, and work from there.
That said, while Paladins are Lawful Good in both AD&D and BECMI, I suppose there really isn't any reason to assume that you couldn't also have a Lawful Anti-Paladin sort of sub-class at 9th level that has basically all of the same abilities as the Paladin, but is Lawful and serves the cause of Evil in order to approximate the Knights of Takhisis. You could either just change the alignment requirement of the Avenger to Lawful or change a few of the items in the Paladin description (notably the "good" part of item #1, and the requirement to assist any being in need of help from item #6. You could arguably also change the "Turn Undead" ability from item #4 to Control Undead, but really- at that point- you might as well just make it a Lawful Avenger.)