There is a difference between refusing to do something, and making someone else uncomfortable in their beliefs. Otherwise every person who holds a belief is a bigot, discriminates, and is down right hateful, which would make the sting of the rebuke a mute point.
Not really. The point is that if you have a commercial business, and you cannot separate your 'beliefs' from your actions, then you still do not have the right to discriminate against others. If your beliefs cannot support your not discriminating, then you should not be running a business. So you cannot be forced to make a cake, but you have done harm to innocent victims in your refusal. And in doing harm to innocent victims, you should be subject to penalties.
And the reality is that the baker can't claim Christianity as a defense in the first place, since he explicitly is not a Christian.