I was toying with some different layouts in Montezuma that require the featured images (post thumbnails) to be loaded as single images with no JS behavior.

As it is, the theme applies two images (one desaturated, the other in full color) and swaps them on hover using JS. I already made one workaround that hides one of two images and uses pure CSS to achieve the color change effect on a single <img>. But it's kind of ugly since I have to use CSS hacks to hide one <img> and force the other into submission using !important rules.

I have a new layout that could do without the thumbnail-controlling JS altogether. Any way to permanently turn that specific JS off?

You can edit postformat.php to remove the post-thumb div from around the image. Then you won't get the desaturated image at all. Or you could call the_post_thumbnail() instead of bfa_thumb(), that will also prevent the desaturated image from being created.