Re: There's a lot more that can be said...
a) put it in a row of many similar other airliners
b) crash it into dense jungle or deep snow
c) land it carefully on a deep part of the sea so that it does not break up, and let it sink intact.
d) Put it in a (big) hangar
Are there any abandoned USSR airstrips in Khazakstan or thereabouts, with bomber hangars still roofed? (Or nuke-proof hardened aircraft shelters, probably good against weathering for longer than the Pyramids) Have all such airfields been checked on the ground by now? (How cooperative are the Stans? )
Still not my favorite theory. Flying Southwest (on auto-pilot? not?) until the fuel ran out is the most mundane way to disappear. It's a long way from land, always very rough ocean, and off almost all shipping lanes. How / why? We may never know.
e) Cut it up and put the bits in (a) scrap-metal compactor(s). I can't conceive of a reason, but if you had the manpower and plant normally used for demolishing buildings and crushing cars, I imagine it could be unrecognisable within a few hours and gone after a few more hours. One for the conspiracy theorists, I think.