The short answer is that Marcus Aurelius wrote his Meditations in the Greek language, and the Greek word for 'Jupiter' is 'Zeus'.

Now, why? Because Greek was the second language of educated Romans, especially when they had an interest in philosophy, as philosophical literature was developed within the Greek language and culture. It was to Marcus Aurelius a sign of culture and high education to use Greek. Compare it with today where people all over the world write books about computers in English: it's the language of that field, its technical vocabulary developed within English.

But why does he still use Zeus? Ever since the Roman Empire expanded into Greek territory, the gods Jupiter and Zeus have been essentially identified with each other: the King of Gods, residing in heaven and occasionally sending lightnings to Earth.

This makes sense, as they both go back to a common Indo-European deity called *Dyḗus ph₂tḗr, Father Sky. In fact, the Ju- in Jupiter and the word 'Zeus' are cognates, i.e. words in different languages that go back to the same word in those languages' common ancestor; in this case, *Dyēus.

Another thing is that Zeus within the Stoic philosophy takes a special role and, as far as I recall, is not exactly the fellow with beard and lightning, but the cosmic force that keeps everything in place. I don't know the extent of that, and I don't know if one can substitute the Roman Jupiter for him within that context.

For further reading about the Indoeuropean pantheon, I recommend M. L. West: Indo-European Poetry and Myth. Oxford 2007.

About Stoicism, our friends from r/stoicism have a sound compilation of ressources.