Given that the three leaders of the guilds are aware of how the world has shifted, Leo wouldn't face any immediate, large negative consequences. Atomight remembers the Fantastic incident, he won't blame anyone for wanting to leave during that time period, nor would he think twice about others coming back to the Alliance.

Some lower level Alliance members may side-eye Leo for his decision to flip flop between guilds. He may also have Society members giving him a harder time when they spot him on the streets, but at this point in time, there will not be any large consequences.