Its not as clear as you state. The ISA were good guys all along. Visari was a modern day Hitler and Helghast the Nazis. That is how the story was showcased in KZ1. Visari's Helghast shot anybody who resisted them, even if they were Helghast. They shot them on point blank range. THey were not patriots or anything.
"Our enemies at home have been re-educated !"
There were people on Helghan itself who resisted and backed ISA like Hakka in KZ1. The Helghast wanted to capture Vekta too, so the ISA forces came in to protect humans.I am not aware of Liberation story, so I can't comment.
It was only during KZ2 development, when the fight went to Helghan that GG started building alternate views to the story. They changed stuff around and Helghan became the name of a company who worked on the planet "Helghan" (THe planet being named after the corporation). And then GG mixed economics in to show that ISA had $$ interests in controlling Helghan and all.
In KZ1, the Helghast were shown disfigured by the Helghan climate, even Hakka and Visari, hence all the mask/goggle issues. During KZ2, they said that the mask was a uniform of the workers and had stuck on as a symbol of revolution that Visari had spearheaded in Helghan. But look at the "enemies at home" in this video from KZ1: they are also wearing those goggles, whereas KZ2 said that those goggles were a symbol of the revolution.
You will find many more story points which were changed during KZ2 development to make the story feel more complicated and intricate.
But this was not the case all along. This shift in attitude that Helghast are just oppressed humans came along while KZ2 was being developed. I think, that is the reason it wasn't fleshed out in KZ2, as the story was pretty different earlier. I think it will be fleshed out more now in KZ3 as the devs are more clear on what direction they need to take. In fact , when KZ2 was announced, me and other people who had played KZ1 were expecting to see some kindof Helghast rebels who would fight alongside us on Helghan to dethrone Visari, as he was a dictator, a tyrant in KZ1. It never happened and instead Visari was shown as Hero of Helghan in KZ2. it didn't really match with the storyline of KZ1, but well, I guess they were changing stuff to make it more interesting. They made it seem that ISA were fed with a wrong image of Helghast. It seems they themselves were a little unsure while making KZ2, it must have been sorted out by now.
We can hope for a better story this time and the trailer seems to confirm that.