For a non-invasive method, I would think a treadmill-type device that mimics the avg. time a turtle requires to reach water, and whereby you measure VO2. There is a ton of literature on VO2 and metabolic rates. Try F. H. Pough, RE Gatten or SJ Beaupre. ALL are on RG.
FAU thesis at http://fau.digital.flvc.org/islandora/object/fau%3A3987/datastream/OBJ/view/Quantifying_the_energetic_cost_of_disorientation_in_loggerhead__Caretta_caretta__and_green__Chelonia_mydas__sea_turtle_hatchlings.pdf