Baking soda accident in pretzel dough - Can it be salvaged?
I made this same mistake because I didn't read the directions all the way through.  After realizing what I had done, I did a search and came across this post.  Since I didn't see a response about going ahead and baking anyways, I decided might as well.... I can report back:

WORST. PRETZELS. EVER.

They were extremely bitter and performed terribly in the oven. I cannot describe how bitter they turned out, but compare it to how bitter bitter melon is, douse it in kerosene, light on fire, then put that fire out with baking soda and there you have it.

=€