The way to do this is to add a confirmation screen. When you attempt to lock in a ban for a champion being hovered by an ally, it brings up a confirmation screen.
"One of your teammates intends to select <insert champion here>. Banning champions that teammates intend to pick weakens the capabilities of your team and can cause toxicity in game. Are you sure you want to ban <insert champion here>?"
And then it has options for "Yes" or "No". Maybe make the buttons say more to discourage banning allies.
"Yes, I enjoy playing with toxic teammates who feed."
"No, I prefer for my teammates to be friendly and play well."
That way, if a champion is being hovered by last pick and is horribly broken and heavily prioritized, players have the option to ban it away anyway. However, it gives warnings that you're banning out your allies to ensure that anyone who bans out their allies is aware of it.
Also, a feature that tells Riot that the reporting player was hovering a champion and the reported player banned it away would be useful too. That way players can report allies who ban away champions, and Riot can look at pick rates/ban rates/win rates of the champion in question to determine if it was legitimate or a troll ban.