One wonders. Plenty of Superman characters who debuted in other media have been introduced into the comics continuity over the years (Jimmy Olsen first appeared in the radio series, as I recall, for instance, and Livewire made the jump from TAS to the comics). But very few originated in live-action film or TV. The only ones I can think of, really, are Zod's sidekicks Ursa and Non.
As depicted in the comics, those two bear a passing resemblance to their live-action counterparts--Non is a hulking brute with a beard, and Ursa is a tall, slim woman with short dark hair--but they don't seem to be what you would call likenesses of Jack O'Halloran and Sarah Douglas.
(Indeed, Non is usually portrayed as bald these days, though he's been shown with hair in the past.)
So drawing Chloe Sullivan as a cute, petite blonde with short hair without overtly resembling Allison Mack seems like it should work. But who knows what legalities might be involved?
Me, I wonder if there's much chance of seeing Chloe in the comics at all. If we did, I suspect it would be along the lines of the plan previously mentioned--she might be Lois' younger cousin, but probably not a friend of Clark's from his Smallville days. It seems like Johns' Secret Origin
will probably be akin to much of his recent Superman work: strongly influenced by the Silver Age mythos, with a dash of the Donner films thrown in for good measure. If she turned up at all as someone from Clark's teen years, I'd expect little more than a name-check as one of his classmates.
I'm not saying I wouldn't enjoy seeing Chloe inserted into Clark's past, mind you; I just don't feel like it fits with Johns' direction on this.