I think we worry about onomatopoeia too much because they’re a bit more codified in Japanese than in English. And sometimes they’re vital to understanding a sentence. But I think it’s worth noting that there are… sort of two types of onomatopeia. Or, two ways to use them. I’m going to use English for the example.
“I whacked him.”
Ignoring mob-related killings, this means to stike someone. The word whack is based on the sound it makes when you hit someone, but that’s really not important here - it’s functioning as it’s own word, and you need to know the word to understand the sentence. Japanese does this a lot. You can ドキドキする and ニコニコ and こっそりと近づく and such.
However, there’s also just sounds that are sounds. “The blow landed with a whack!” is an example. In this case, it’s just the sound effect. You understand what it is, because the sentence basically defines it for you. I don’t think we need to worry about these - even when they’re the same words - as much as the former, but I see people worry about them a lot. I especially think we shouldn’t because this use is more likely to involve innovation. Think of comic book (or classic liveaction Batman) sound effects, all thwip! Kachunk! Sproi-wong! Bamph!
These often aren’t as codified because they don’t need to be - the situation tells you what they mean.
ミキミキと鳴る is falling solidly in the second camp. We already know what the pillar is doing in a strong earthquake. We don’t need a definition.