The use of the Past Perfect is appropriate in your example.
But because it's inside a Relative Clause and with the Adverb "just," it doesn't really make much of a difference if you switched to Past Simple, because the context is perfectly clear.
Ex. Yesterday I saw my friend who JUST FINISHED university and...
Ex. Yesterday I saw my friend who FINISHED university and... (more
general meaning of "finish university," not recent)
If you really want to see and pinpoint the difference between using Past Simple and Past Perfect, you could try something with no Relative Clause and with a more dynamic Verb:
Ex. Yesterday, I saw my friend. He HAD WALKED OUT OF the school gates
Ex. Yesterday, I saw my friend. He WALKED OUT OF the school gates and...
Like what you said, the Past Simple in the second example can make the story a series of actions and make the whole meaning awkward.