Kill her? don't let her unleash her full combo on you (2 rotations of her abilities)? Don't let her get so ahead she can 100-0 you in one short combo?
Buy early MR or Health? Purposely pick a champ with good CC and counterburst? Even if your hard CC is a skillshot (Like Morgana's Dark Binding) she's got to get into melee range to do anything but poke you, and she'll signal it quite damn hard when she's about to so you should have a good idea of when to be ready to fire it off. Then when you've CC'd her, you unleash your own burst and walk back to your tower.
Or you can pick a heavy poke champion and poke her away from early CS.
Or push the wave and force her to CC under the tower while you run off to gank other lanes.
If you let her get so far ahead of you that she can instagib you that easily, then you're either letting her get away with too much in lane, or your matchup is horrible.
Akali has pretty clear weaknesses, so if you want to guard against her you pick a champ which can exploit those weaknesses. Or you focus on how your pick can do something, and how building stuff you wouldn't against a champion you're not weak against can impact oyur performance.
Of all the things people cry about with Akali I never see anyone pick on the things that are actually kind of overloaded on her kit, namely the spammability of her ult and the non-interactiveness of her E.