I think the problem here isn't so much what the guitarist done, instead it's the lack of communication.
As to the parts, listen to the song instead of just the bass. It could well be that it DOES sound better. I've had to take a step back on a couple of my lines in realising that. It's a bit of an ego hit but it's not about my ego or anyone elses for that matter, I just want the songs to sound good. Sometimes that means not playing a fancy little run and sometimes it means playing your arse off with lines that you struggle with.
I really suggest blind testing the tracks to someone that doesn't know them and ask what they think. Don't tell them to listen to the bass beforehand though.
If you want to still be on the album (this would be my issue) re-record but with you playing the new parts if you agree they sound better. My guitarist suggests bass parts to me, I tweak and send them back, he listens and suggests, I listen and try etc... I then suggest slight changes to the guitar part and so on and so on.
Overall, don't get down about it. Atleast there's some enthusiasm going on