"It is thundering."
天動(script 天动)? This should be 천동 though, indeed it seems it used to be. 動天 means heaven-shaking/earth-shattering in Japanese, so this would be more the shaking heaven/shattering earth.
The equivalent of 번개 in Japanese means lightning and thunderbolt, but only 뢰(雷, synonym of the above in Korean) means thunder as well, y'know, the reverberating rumbling sound of a strong one that shakes the ground.
The Namuwiki (나무위키) agrees with you, but without providing sources and i haven't been able to find any myself either (at least not at a quick search).
It's possible that 천둥 indeed originally came from 天動 (which, yes, should in theory be 천동). There are words which are confirmed to be 한자어 but still have deviant readings (for example 秒 "second" which regularly should have been 묘 rather than 초). But it's also possible that it's a native word which just happens to look like 한자어 and there also happen to be characters which seem to match. That too happens at times (e.g. 생각 looks like it might come from 生覺 or maybe "corrupted" 醒覺, but it's actually native).