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A traditional school, or darshana, cannot be “intrinsically heterodox”, though Vedantin that you are I can see what leads you to this question in regard to Mīmāṃsā.
The denial of a deity—or rather the suspension of judgment as to whether there is a God or not—is characteristic of Buddhism, as we know. In the Vedic context couldn’t the “atheism”, or better “non-theism”, of the early Mimamsic authorities to whom you refer simply be tantamount to an affirmation of the penultimacy of every concept of “Lord”?
As for their denial of the yugas, is this anything other than a recognition that, even though things may seem to be passing through cycles, this cannot really be so, time and flux being features of Māyā? After all, from the “point of view” of the Absolute, to use the uselessness of such a phrase, pralaya and manvantara—”day” and “night” in the “life of Brahmā”—are simultaneous.