LF knows that Harrenhal is a poisoned chalice, so hasn’t used it as anything other than a stepping stone to get himself in range of marrying Lysa so he could get his hands on the Vale.
As for why Cersei’s ok with it, well, it allows her to have her cake and eat it too – the Lannisters get Littlefinger’s loyalty (at least on the surface), but can keep giving Harrenhal to their other followers (Gregor, etc.).