As long as there is a visible prompt or other explanation informing users that they must install IndieAuth to user Micropub or Microsub, I’m in favour of removing the fallback.
For what it’s worth, I think IndieAuth is reliable enough that supporting external auth is no longer needed. If there are cases where people have trouble getting the IndieAuth plugin to work for them, then a fallback is handy. However I think you’re correct that the added work (and complexibity) of maintaining secondary authorization methods across multiple plugins is not ideal.