The arguments against auto-tune are typically different, since it's obvious to anyone that autotune can't make you sound like a soprano if you're nowhere near - so skill is still required.

The problem with autotune is more that it removes a lot of nuance from singers' voices, it's like listening to MIDI instead of listening to a real piano. This is, however, something that can be improved. Synthesizers can produce wonderful musical effects, and there's lots of highly virtuoso music on synthesizers (including voice distortions, pretty similar technically to autotune) for those that are into it. Progrock, for example, was all about using new technology in complex and extremely interesting ways. Maybe more interestingly for your particular objection, you can look at early electronic music, say Vangelis or Isao Tomita or Kraftwerk. For at least parts of their songs, they could have just programmed their synthesizers ahead of time and played concerts without even being on stage - but that doesn't take away from the fact the music itself.

Ultimately, if the music sounds good and elicits some feelings and thoughts, it's good music. Whether the musicians can reproduce it live or it's done 90% in a studio doesn't really matter here. Of course, it does mean it may not be worth going to a live show from some particular performer, and it also means that the performer is not necessarily the most relevant artist - the person programming the "auto"tune should at least be considered part of the band.