I think you make a fine analysis, but I would just offer that real life can be quite jarring and uncomfortable. So a story which paints a very real picture of life (rather than constructing a narrative) might just be unpleasant. I don't think her story is poorly written, and I think it is quite memorable.
For reference, I also really enjoyed the Catcher in the Rye, and there are some superficial similarities: a young person is scarred by events in their lives and succumbs to depression. (there are a myriad of differences between the two stories -- I'm not drawing an equivalence, just making one comparison)
Catcher in the Rye is probably best read as an angry teenager: you meet Holden Caufield and he's witty, cynical, funny, defiant, etc. You might fall in love with the character, but what you ultimately learn is that he's a miserable failure; he lost the battle with his depression and so many of the people he was cutting down were just normal, decent people trying to enjoy their lives.
Crucially, we never meet Holden when he is young, bright eyed, and innocent. The narrative structure shows us who he is right away, and we the reader learn that this is actually quite a bad thing throughout the course of the story.
Persepolis works a bit differently: we spend the first half of the book with innocent, bright-eyed Marjane and we fall in love with that character. The character we fall in love with is taken from us by the events of the story, by living unsupervised in exile, etc. It's nothing but sad. It's well-written, it's very memorable, but I don't think there's anything wrong with feeling unhappy about an unhappy turn of events.