I have really loved this lore event. It was an awesome change of pace to League in many ways, but this statement is scary to me. What constitutes cool to the lore team may or may not be cool to the people playing these champions.
Lets say they have a Piltover event where Jinx Caitlyn and Vi all 'die' in an explosion. I would be out my two best ADCs and my most played jungler. True that I would have 123 other champions to play, but even if they were only disabled for a week I would effectively be banned from ranked for that week. That is not immersive, just annoying.
Another perspective to look at it from is a new player. Players from the level ranges of 5-20 have not yet played enough to have a diversified champion pool. Any newer player with a champion the lore team has disabled for the 'cool factor' now might have a significant portion of their champion pool disabled. Hardly an incentive to keep playing if they find Riot will just take away their champions for no better reason than lore they have not yet played enough to be invested in.
This kind of thinking also disregards the financial aspects of lore disabled champions. Skins cost money. At any point in Riots history when a player acquires a skin it is done so with the knowledge they will have access to it from then on with the standing exception of being when a champion is selectively disabled due to a game breaking bug.
Is Riot now saying they will take away our ability to use products we have paid for because they believe it enhances their story telling? That is not something I am comfortable supporting as their are many games (read nearly all) that would not make this kind of statement.