Learn English – Why is the word “being” used as a suffix with “human”

Rupt is better thought of as a word root than as a prefix or a suffix. It comes from Latin.

Rumpere is a Latin stem meaning "to break". From that comes the Latin ruptura, meaning "fracture".

As you noticed, these words are connected in that they all seem to describe something broken.

Here you'll find a more detailed etymology of many words that contain the root.

The Online Etymology Dictionary may be right, but unfortunately it gives no citations in support of its claims. Being does indeed first appear as a noun in the fourteenth century but in the sense ‘a living creature, either corporeal or spiritual; especially a human being, a person’, the OED's earliest citation is dated 1666:

If there were no Sensitive Beings, those Bodies that are now the Objects of our Senses, would be but dispositively, if I may so speak, endowed with Colours, Tasts, and the like.