Application of Alodine can be done in-situ, but one must exercise caution to ensure the solution does not find its way between surfaces that cannot be disassembled & rinsed. The Alodine 1200 or 1201 solution (the oft-used "gold" colored mix) is a ferro-chromic acid solution that performs a controlled chemical reaction / oxidation of the aluminum. The reaction is stopped by removal from the Alodine, and a rinse. If Alodine wicks into areas where it cannot be rinsed off, a decent corrosion problem can be established. Think of Alodine wicking up into the canard, on the lift tabs. One could not remove the Alodine up in the structure, and further etching would occur.
In the field, application of such treatments in-situ is often done with paper towels placed on the area to be treated, and wetted with the Alodine. It does work, but one still has to be careful. Any situation where gravity or unwanted capillary/wicking action must be eliminated when doing an in-situ treatment.
For anything on our airplanes that cannot be removed for treatment, I'd suggest applying a good primer (zinc chromate is very good) followed by a compatible enamel topcoat or epoxy paint. Or, simply use a good primer that is compatible with aluminum and the rest of the airframe, as part of the overall painting effort. Don't worry too much about Alodine application at this point. Also, in any areas where an aluminum part penetrates into a glass layup, use a good automotive urethane seal to fillet-seal the penetration. Do not use ordinary silicone (RTV), as the acids in the uncured mix are probably not good on aluminum. For completely enclosed inserts (e.g. the hardpoint inserts in the Long-EZ wings & center section spar), I would not worry too much about those rotting away - they are pretty well isolated from Ma Nature's fury.
For my VariEze wing fittings, they have complete periphery seals made from a chromate-based aircraft sealant (ProSeal). I do not ever expect any moisture penetration into the fitting-to-sparcap intrface areas because of this. Not everyone can get ahold of small quantities of such sealant (I work for Boeing...), hence the suggestion to use a good automotive urethane sealant (available at most auto body & paint stores).
Hope this helps some.