Maybe against Steppenwolf he could have said "Hey, Darkseid, have your dog back and go away", but in the first two its not like he had much useful options with Zod or Doomsday, so, yeah. There's a reason traditionally some version of the Phantom Zone has been available to Supes.
(Otherwise known as my agreeing with you, if its not clear. This is why I say the problems with Superman's situation in those movies were less problems with his characterization than him being placed in impossible situations (especially in MoS when, as I noted, he's been operating as a superhero for about ten minutes) by writing choices. So its less his characterization than the conventions that normally surround him being ignored).