First let me point out that you can flag anything you want for any reason you want - that doesn't mean the flag will be marked helpful :-)
Yes, this can certainly be a valid reason for flagging.
If someone asks a question about Harry Potter which specifically requests no spoilers from the last 2 books (or 3 films), and someone else leaves a comment which says
Snape kills Dumbledore,
then that person is being a jerk (or possibly didn't read the question properly, but either way the effect is the same). You'd be perfectly right to flag such a comment, and personally I would delete it if I was the one handling the flag. Comments aren't meant to be permanent anyway, and if a comment is unnecessary and obviously going to piss off the OP, then it goes.
With the specific example you cite, I wouldn't say it's completely clear-cut. The commenter said:
Excluding preview chapters is a bit silly, as there's at least one character off the top of my head that is confirmed alive in the preview chapters while you list them as being dead.
The OP had listed several characters as being dead, so this isn't a massive spoiler as it's not clear which one the commenter is referring to. That said, if it had been flagged I would still probably have deleted it.
Per the comments, you would use a custom flag reason of
other... and leave a message of:
this comment contains spoilers that the OP specifically asked not to be told
or something along those lines. It may be helpful to also include the URL to this meta topic, so that any mod handling the flag has easy-access to this discussion.