I haven't watched this Primer, if it is important.
It is. My comment is only funny if you already knew that the movie being identified was Primer, which it was, and knew about Primer's reputation as a very difficult movie to understand.
Is it kind of a pun?
It's not a pun, no. There's no strange word play going on here -- the words all mean what you think they mean. However, you do need to follow the chain of reasoning all the way to the end to "get" the joke.
Why is helping the friend identify the movie the opposite of helping?
"Identifying the movie may lead to your friend watching the movie" seems very logical to me, it is exactly what she wants, isn't it?
Here you skipped the part where the "punchline" was:
- The first part - identifying the movie - is fine. That is definitely helping.
- The second part - watching the movie - is also fine. That's very likely what the questioner's friend wants. So, that's also helping.
- The third part - trying to figure out the movie - is the problem.
Primer is an incredibly complicated, non-linear movie that involves time travel, and in particular, experiencing the same set of events occurring in multiple timelines and largely out of order. You don't really figure out the opening scene until very close to the end. Even then, trying to trace exactly who's doing what to whom at each point isn't even always possible. That's not counting the complex mathematics and engineering shown in the movie.
The "joke" is that, showing your friend this movie may lead to them going crazy trying to figure it out, which could "hurt their brain", and that's definitely not helping.
In addition, the comment was worded that way ("the opposite of helping") because of the way the question was worded:
Can anybody help my friend by identifying the story?
Thus playing on the somewhat counter-intuitive idea that doing what the OP has asked may have the opposite effect to what the OP is expecting.