What you say here is true, but misses the point. Riot loses little when they permanently ban a toxic player who happened to have paid money for content. It can be reasonably argued that Riot gains from doing so, by improving the player experience such that other players are more willing to purchase RP. Indeed, an incredibly small fraction of players are permanently banned. Most people don't care that the toxic player receives no recompense, or that the toxic player is upset that they receive no recompense.
When Riot changes the runes system in the upcoming preseason, literally every single active player will be affected. If Riot chooses to provide no compensation, they create a LOT of consumer ill-will. It's a completely different situation. Instead of a tiny fraction of upset people, you suddenly have a near-universal percentage of players upset at a lack of recompense.