I actually agree with Othello. Chloe was a minor, non-canon character that was never supposed to become so important. She was only supposed to be the exposition character, who spells out whatever the audience is (apparently) too dumb to figure out on their own. Superman doesn't have a sidekick, and never needed one,but somehow once she found out, she made herself that, and proceeded to take over thinking for him. That's bad.
This, however long it lasts, will be a good thing for him. It will force him to USE that Kryptonian brain of his. Kara showed us what could be done with one (sucks that she was cut out). I don't know if Chloe will or will not get the memories back, but it's long past time for the apron strings to be cut.
As for the holes in her memory, I'm hoping for a scene sometime that addresses that. If it doesn't bother her now, it should at some point. There 's a lot of stuff that won't add up (like why Lex fired her). But this is Smallville so I don't hold out much hope for that.