The phrase “jump for joy” pretty much means, “jump with joy,” although, as the commenter said, it often refers to figurative joy without literal jumping.
The fans jumped for joy after their team won the championship.
If I read that sentence, I’d assume that some of the fans might have literally jumped, but others may have simply shouted and cheered instead.
As for your more general question (How can you tell which meaning of “for” is intended when there are so many to choose from?), prepositions are notoriously difficult to explain and pin down. Often, the meaning of the specific word is vague, and may even overlap with another preposition, such as with or on. For example, when I say:
This happened for no good reason.
that’s pretty much the same as:
This happened without a good reason.
Other times, the meaning is more idiomatic; for example, if I say:
For the time being...
As of right now...
I wish I could share some nugget of wisdom that unlocks this mystery, but all I can say is that you’ve identified a thorny challenge for learners: there’s no reliable, magic way to figure out which of the dictionary’s several meanings will map to the one you’ve stumbled across.