? do you mean just for handling and forming, or for final installation ? i assume you're talking about clad Al. i'm not sure when in the part manufacturing process you'd "destroy the Al coating". in any case, Alodine application is an acceptable process for restoring the corrosion protection.
i think we remove the plastic film early in part manufacture, and alodine as required, and prime, and top coat as required. i'd be uncomfortable leaving the film on the component, mostly 'cause i think this is un-common practise (and has a bunch of unknowns).