Since I don't know the voices, I can't really tell much about the auto tuning.
Technically, the vocals cut through well, and the lyrics are intelligible. There's a too much processing on the guitars as you say, and that probably forced the engineer to use a lot of compression to get things to sit right. You guys did a good job performing regardless of the other issues.
It's hard to make two strummed steel string acoustic guitars sound interesting, so maybe that's why the guy messed with them so much. For a recording, it might have been better if he'd simply had one of you try a Nashville tuning, or play a 12 string, or try a nylon string, to keep it natural, instead of messing with modulation effects.
A standup bass might have balanced things out for the recording, too, in a natural way.