I think it's safe to assume Lea is firmly a good guy now on the side of Sora. I think the real turning point for him was in 358/2 Days when he realized just how bad the Organization really was and what extremes they were willing to go to (Eliminating either Roxas or Xion), though given he did forget Xion after 358/2 Days, but regardless the feelings of distrust toward Organization XIII must have remained there in some form.
Through out KH2 he eventually ditches Organization XIII and begins working toward his own goal of bringing Roxas back. However, by the end, we know from the novels that off screen Axel attempted to rescue Kairi from the Organization, but was stopped by Saix and injured from the fight. After that he went to help Sora in Betwixt & Between where he sacrifices himself to help Sora make it to The World That Never Was. It is clear at this point that he has joined Sora's side, otherwise he would not have risked his life to rescue Kairi, because rescuing her served no purpose in getting Roxas back, so he must have did it because he switched to Sora's side.
So him joining Sora and the others as Lea in KH3D really should not be surprising. At this point he is as much a good guy as Riku, Mickey, Donald, Goofy, Sora, Kairi, Yen Sid, ect.
The real question is where are the loyalties of other members such as Ienzo & Eleaus? Now I personally believe Ienzo, Eleaus, Demyx's original, & Luxord's original will side with Sora. (The latter two due to their friendly terms with Roxas in 358/2 Days). Dilan & Even I think will be seekers of darkness. Finally Marluxia's original & Larxene's original will be on neither side, they will be out for their own goals but will help Sora temporarily since both sides consider Xehanort their enemy (Marluxia's attempt to betray Xemnas in COM).
and to do that get on sora's good side i guess :/
