If Konoha was all about the Will of Fire, team work and never leaving behind comrades in need, why was Sakumo Hatake punished so bad? There's so much emphasis on being there for your team members, I don't understand why Sakumo Hatake was looked down on for saving his comrades and abandoning his mission, to the point he committed suicide. It's a part of the story I find inconsistent.
It wasn't the fact that Sakumo chose to save his comrades that lead to his disgrace. His decision to abandoned the mission caused the mission to fail, which was supposedly very critical for Konoha for it to succeed. His allies (Konoha and those who he saved) blamed him for the loss, which lead to his suicide.

This is covered in Naruto Chapter 240.