It’s hard to really root for Zeon in Gundam, and whatever Harutoshi Fukui’s political leanings may be, I don’t think that’s what Unicorn attempts to do. Despite how humanistic the Zeon characters are in this show (especially compared to the cold, inefficient Feddies) and the damming account of Feddie occupation, Zeons atrocity during war-time still casts a massive shadow over the episode, both in the colony-drop and by showing the Shamblo decimate that random Australian suburb.
As you point out, this more human portrayal serves simply to give a richer, more fully realised lore. It is clear in Unicorn that spacenoids are, to an extent, disenfranchised. They lack the right to vote, they were occupied and pillaged by the Federation (which recalls Mineva’s comment about Spacenoids being used to violence against them). I’ve even heard that in the novels it is explicitly mentioned that the spacenoids are classed as abandoned refugees by the Government, which is why they lack certain fundamental rights. This doesn’t justify the gassing, the colony-drop ect, but it does make it more believable that so many spacenoids would be attracted to such an extremist organisation as Zeon. I hear a lot of complaints about this series being “Zeon fanwank” or whatever, but I actually think it does a good job of making the ideologies of UC as a whole much more fleshed out and believable.
And any time it gets a little too “Hail Nippon!” or “those evil FEDDIE Amurrikans!”, Banagher is there to give Zeonic ideology a good hard kick in the balls.