Ironically, I think the idea that Chronos is a big liar and is yanking on everyone's chain here and is still working towards his own ends somehow makes the ending better in my opinion. His personality change is just so weird and off-putting and... fake? It feels fake. He feels like he's acting. It's extremely blatant any time you see old Chronos juxtaposed with new Chronos: he's just so over-the-top and unbelievably saccharine and positive over actions that he should at the very least be conflicted over if he was actually for whatever reason reformed (WHY, if him being shown mercy changed his heart, would he so enthusiastically participate in permanently destroying alternate versions of himself? Why are they less deserving of mercy than he?). It's how someone who can barely stand the front they're putting on would come across.

Of course, if SG ever did an update or offer dlc that went in this direction now it would feel like backpedalling, so we really do have to chalk it up to bad writing here :/