Always figured it was a new direction they were going for, as "joining the league" can seem something of a stretch as to why some are fighting (or allowing themselves to be used to partake in a fight). Since it's a "Works for everyone" kind of deal, who would stop them? Using Nautilus as an example:
"Terrified sailors whod heard his tale directed Nautilus back to the Institute, but the summoners refused to relinquish the names of the others they commissioned. By then Nautilus had learned about the League of Legends and there he saw an opportunity to discover and punish those responsible for the time and life he lost."
...is solid for a short lived commitment, but possibly not a long one (like how Naut can go elsewhere to dig things up on the Institute of War, or how rejoining the very orginzation that allowed him to lose his life is counterproductive).
On the flip? Soraka and Warwick's new lore suggest that they don't have any allegiance to the Institute of War, Soraka just wants to help people in her mortalhood and Warwick just wants to rip her heart out. Kha'Zix and Rengar just want to tear each other to pieces and Syndra just wants to destroy Ionia's elder council. There's aggression here that's used (and played up) in the game that shows that these individuals could just be using the League as much as the League is using them (in a sense). But I don't know.
League's lore does need a good way of being conveyed better in some cases. But it does look like things are beginning to be more coherent while evolving/changing.