3: I thought you would eat
4: I thought you would have eaten
...where #3 implies ...but I see you are not currently eating, and #4 implies ...but I see you did not eat earlier (in both cases, I thought something, but I was mistaken).
It just so happens that the Unmarked Infinitive and the Past Participle of to come are the same. But just as in my example, OP's #2 refers to an action that I thought would have already happened in the past. This leads to the likely (but not "fixed") interpretation that #2 refers to an occasion in the past when the addressee did not attend, whereas the most likely interpretation of #1 is that the addressee did just arrive (if not, he wouldn't be there to be spoken to! :).
Note that the difference between whether the speaker's preconceptions are/were confirmed or not primarily turns on whether stress is placed on thought or you (implies you did come; my expectations were confirmed) or on the word come (implies you didn't).
So what I wrote above about "likely" meanings only applies to a written text considered in isolation (with no context and no indication of stress patterns). Real language is spoken, and in practice there would be no ambiguity because native speakers would always indicate the intended meaning by the choice of which word to stress.