While I'm not sure how well it would work on a plastic model, Krylon makes something called Workable Fixative that might protect it without being invasive like some of the other suggestions. It's used to seal drawings (like charcoal and graphite), but you can work over it afterwards. Might test it, because I suspect it would be a much more subtle sealant.
Or, you can get a pellet gun and destroy your model ship like it's supposed to be destroyed.
Edit: it can be used for plastic....
http://www.michaels.com/Krylon®-Workable-Fixatif/cp0411,default,pd.html