The protagonist, Qin Yi, was not a child with overflowing compassion, but a clear-headed soldier with a heart of stone.
He was influenced by the consciousness of the Zergs and naturally felt close and sympathetic to the Zergs. However, he could use his own rationality to resist and reject this feeling of closeness. He lied to the Zergs without any hesitation and ordered the extermination of the entire Zergs. This was what the protagonist of China should do.
Of course, this made the ending seem even more ironic.
If it was a saintly protagonist who called for peace with the Zergs and ended up on the Zergs' side, the audience would only think that he was a 'human traitor' and an idiot. They would not have any good impression of him.
However, Qin Yi was completely on the human side. Yet, he had been betrayed by a freak combination of factors and had no choice but to become the ruler of the Zergs. This made it difficult for the audience to hate him.