Both sentences make sense, but I would change the first one slightly.
I can't work with you if you're going to be so obstinate.
We would often use 'so' in sentences like this.
Here, 'so' means 'to this extent'.
You could also change 'you're going to be' to 'you insist on being'. Using 'be' in the continuous form emphasises that this behaviour is annoying.