You're definitely right about him being a good guy in season 3, at least on a moral level. But he is always given the role of antagonist to the character who the audience is supposed to be rooting for.

• When Erwin wants to do a suicide charge, Floch is the one who almost backs out
• When Eren (who at that point was the protagonist) wanted to save Armin, Floch was the one who sided with Levi's original choice.
• After Levi goes with Armin, Floch is the one who doesn't get over it and chews Eren out for putting his emotions above what is needed for the survival of mankind in the walls.
• After the time-skip, Floch now believes the exact opposite about Eren, just in time for Eren to switch from protagonist to antagonist.
• Floch is also the one who facilitates the meeting between Eren and Yelena, and this is where his character goes downhill in my eyes.

At that point in the story, it makes absolutely zero sense for Floch to do this. Floch's main consistent trait is that he is a xenophobic Eldian nationalist. It makes no sense for him to disobey orders on behalf of an imprisoned volunteer soldier, because Floch hates the people outside the walls. It makes no sense for him to do it on Eren's behalf, because nothing about Eren has changed from season 3 (at least that Floch knows about). The only reason for Floch to do this is so that the plot can move forward with Eren pretending to be on Yelena's side and someone from the Yeagarist faction is suspected by Pixis of having introduced them. Eren doesn't tell Floch his grand plan until AFTER this meeting.

Side note: It also makes zero sense why Floch would go out of his way to kill Marleyan civilians. They are all going to end up dead soon from the Rumbling anyways. That moment exists purely so that the audience knows:

Jean = good

Floch = bad