I haven't seen this theory yet. It is an interesting one. Warning: Spoilers Ahead!!!
We know HADES was made as a reset button for GAIA. HADES was supposed to wipe life on earth and have GAIA start over. The main theory is that a signal made HADES go rogue and activate when he wasn't supposed to. What if something DID go wrong? What if he WAS supposed to activate and do a reset? I mean, even the Aplhas said GAIA probably wouldn't get it right the first time. What if she didn't?
If you look at the map and the biomes, you will see that as you get further out everything has less life. What if the forbidden west has almost no life. There are no grazers in the desert. What if GAIA started producing human life too early? GAIA wasn't expecting humans to replicate at the rate they were. We also know that at some point HEPHAESTUS started producing aggressive robots to protect the terra forming robots from humans. Humans were killing machines faster than GAIA could produce. Also, Without APOLLO, and knowledge of agriculture, humans were not helping in the terra forming process as planned. What if HADES detected that humans would out grow the terra forming process so he switched on to reset the whole thing.
Elizabet made GAIA able to feel and have compassion for life. GAIA was almost human herself. What would she do if HADES switched on so far into the process? GAIA succeeded in making human life. She loved her children. Then HADES came in and said nope. You did it too early. We have to kill everything and start over. GAIA would go mad. She would try to kill herself to save her children. That is what she did. She also made a clone of the most caring person she knows to stop HADES and rebuild.
What if HADES was the good guy? And GAIA was the over obsessive mother that does harm to her children rather than good?
Edited: For Format