We know that while Thundara is ostensibly full of life (at least plant life, given the many jungles), there's next to no ThunderCats. Of the ThunderCats, the only living ones are a single pride of militarized peoples with impressive, but limited tech. In fact, there is next to zero non-military technologies in all of Thundara - of which there is little and it is dispersed amoungst much cruder impliments of war like clubs and swords. It's as if their society was destroyed by an advanced civilization and they've picked up the remnants.

We also know that ALF's species have mastered Space-Travel (Alf crash lands onto Earth). So, what if ALF actually worked as a probe; sent to Earth to report on his findings of valuable products? It would make sense; if he were on a mission to study Earth itself, he should have been with a party - at the least a Chief Biologist and Geologist. However, as a single-person mission it could stand to reason that ALF was an independent contractor for a Melmacian Goods Company.

If ALF crashed onto Earth, it would stand to reason that the Melmacians have sent multiple probes out to inspect many planets for valuable goods. What if one of those planets was Thundara?
I propose that Planet Melmac held an all-out invasion of Planet Thundara; using their superior technology to easily defeat and cull the Thundarans ala "Signs". During this invasion, a few survivors managed to stave off roving bands of these Cat-Devouring sycophants - these lucky few were the ancestors of the ThunderCats. After the invasion ended; the remaining Thundarans were torn over governmental leadership and broke into two main parties; Followers of "The Old Ways" and Followers of Enlightenment. Reverse engineering a vital few components of Melmacian technology, the Followers of Enlightenment beat back the Followers of "The Old Ways" and killed their leader: MumRa. Through voodoo of The Ancient Spirits of Evil, MumRa survives as a mummy cat-like being and continues his Luddite battle against the technology that destroyed his species and those whom he feels betrayed the Gods (albeit, sometimes resorting to using technology himself, but generally prefering magic). The ThunderCats now spend most of their time attempting to find and reverse-engineer Melmacian technology to better their society in the hopes of repopulating Thundara and perhaps negating a second invasion.

TL;DR - The ThunderCats' ancestors were abducted and eaten by ALF's species and set the stage for MumRa and The ThunderCats to oppose eachother.