On new aircraft designs, easy - just equip the engines with DECUs and incorporate an immobiliser into the design. Actually, sometimes just having the DECUs is enough to immobilise the engines.... Temperamental little devils, they are!
Failing that, a shackle over the skids or u/c, fitted into a ground anchor much like a motorcycle immobiliser would make it impossible to lift the aircraft. Would that be acceptable, at least at home base? Or a metal cover that locks over the engine lever/s for off base ops?
Also, Mr Sikorsky incorporates strong locking doors on the S-76. BTW, Nick, I found out exactly what the source of those locks actually is, when I went to a locksmiths to get some spare keys cut!