I thought Lana and Pete were pretty much just flashback characters that we didn't really see much of once Clark moved to Metropolis? I didn't think Chloe even existed in the comics?
Lana Lang and Pete Ross were characters from
Superboy comics originally, but they were folded into Superman's present-day adventures after a while, with Lana being Lois's main romantic rival for Superman in
Superman's Girlfriend Lois Lane in the '50s and '60s and a TV anchor alongside Clark in the '70s. Pete had a smaller present-day role, but in the early-2000s story arc when Lex Luthor became US president, Pete Ross was his vice president. (Lois's father Sam Lane was his Secretary of Defense, and a retired Black Lightning was his Sec'y of Education.)
As for Chloe, yes, she was created for
Smallville and only briefly added to the comics continuity in 2010. But she already exists in
Supergirl's universe; in "Midvale," teenage Kara and Alex corresponded with her by e-mail to help solve the crime they were investigating. She was described much like the original character, as a childhood friend of Clark's who maintained a "Wall of Weird" involving strange phenomena.
I'm not sure it's necessary to retire the character of Chloe because of what's happened with her actress. That's like saying they should've retired Superman as a character when George Reeves shot himself (or was murdered, as Jack Larson always insisted). Granted, it would be easier to separate them if more than one actress had played the role, but still, the character isn't to blame for what her actress ended up doing.