I would even say that "crossing out lines you disagree with" is vandalism because a book can always be read by others and come to a different conclusion and debate in their mind from there.
Why treat books as disposable mind scaffolds when they can be used again by others productively and even preserved for later generations? If you found a book to be at least somewhat useful to write notes on, then why would others not also find it useful?
Margin notes are fine though as long as they do not make the main contents of the book unreadable like "crossing out lines".