Providing the work load isn't too heavy, it would probably be best to just get the measurements over with. Maybe weigh them now and photograph them in the planes that will be most relevant to the features you are going to measure, those photos may also be useful for geometric morphometric analysis. Alcohol or fixative would both probably affect size and shape as you suggest. If necessary, you could store them in 30% sucrose in PBS for a short period.
Dear Zeiri, the method suggested by Igor is surely the best way to preserve larvae for long time. My larvae, so killed and preserved, are perfect from more than twentyfive years. Just remind to boil larvae from a few seconds to about a minute (according to the size), and only for living larvae.