Clark just did to Chloe what Brainiac was doing to her---erasing and controlling her memory. I think that we are supposed to equate the two things. Clark made a choice and now he will have to man up and face the consequences of that action and choice (Black Day at FOS!). In fact, he tells Jor El that he will. Clark isn't perfect and he doesn't always make the right choices, but he does have the powers to change and modify the consequences. Every dead Chaotic butterfly brings back Brainiac---or so it seems.

Now---what will they do about Oliver Queen knowing Clark's secret? And what about the other one, Lana, who also knows the secret and who was also infected by Brainiac? Chloe is some sort of foreshadowing for Lana. And Lana is coming back!