If someone says: "I am sorry, but I read your diary", it means that person read the entire diary, right? Wouldn't it be better to say "I have been reading your diary" if they want to express they have read parts of it and not everything?
Difference Between Diaries and Other Books
If you were talking about a regular book, then you'd have it exactly right:
I read the book you gave me. [I'm done with the book.]
I have been reading the book you gave me. [I'm not done yet. I'm still reading it.]
A diary isn't like a regular book, though. It's a special book people use to write down their most personal and private thoughts, without anyone else reading it. It's also one that people keep writing in, and these distinctions make the implications of your statements slightly different.
If someone told me:
I read your diary.
I would interpret it to mean that, at some point in the past, the person read any part of my diary. They may have read the entire thing, or they may have just read a part of it. Since they're telling me that they read it, they probably read at least one part they weren't supposed to.
The action of reading someone's diary has more to do with violating the person's privacy than the act of reading it as a book. The violation occurs as soon as someone starts reading the diary, not when they finish reading it.
Present Perfect Continuous
If someone said the following unprompted:
I have been reading your diary.
I'd interpret it to mean that the person not only read a part of my diary, but they kept on reading it over multiple sessions. In fact, there's probably an implication that they've been reading my new entries as I've been writing them.
If they said the same thing to answer the question:
Q: What have you been doing?
A: I have been reading your diary.
The implication that the person read my diary multiple times isn't necessarily there, but it probably means that I just caught them doing it.
Yes, to some extent you are correct. For example:
I cooked us dinner
means that dinner is ready, whereas:
I have been cooking us dinner
generally implies that the cooking is still in progress.
However, given the context of reading someone's diary (a rude invasion of someone's privacy) the present perfect progressive implies that the act is ongoing and -- more importantly -- you don't intend to stop doing it.
As an example, it would be odd to tell someone:
Hi, I have been tracking mud all through your house, I hope you don't mind if I track some more?
Of course you do see people like this in fiction (and occasionally in real life) but most of us recognize it as atypical behavior. In the same way, if you did read someone's diary, perhaps by accident, you want to use the past tense (or past perfect tense) to indicate it's a complete action, and not one you intend to repeat.
I'm sorry, I tracked mud through your house. Let me get a mop to clean it up.