"An anonymous downvote pool could be the solution there - if the whale I flagged can't see that it was me who flagged him, he can't flag me back."
That is a double edge sword, and that 2nd edge would have the opposite effect that you are hoping for.
I would hope for something like this to encourage flagging while preventing flagwars at the same time. Flagging will always be controversial, but taking Reddit as an example, while it can have negative results in some cases where flagging is abused to punish individuals or views, it mostly helps to prevent low-quality posts from reaching high visibility
The ability to downvote away the rewards of others is already one of the worst features here - if you were to allow it anonymously, (and cheaply), you would kill the community.
That was kind of my point.