Wow, a tough situation for sure. It sounds like the chances of a reaction are really small, but the consequence is quite bad. Can you get a second opinion from another doctor?
The other thing to think about is - if it is the live vaccine causing the problem, then if you or LO ever get whooping cough you will likely suffer the same reaction. The you've not only had the reaction, you'll have whooping cough too. So by not having it, you're not really preventing anything as there is still a chance it will happen if you catch the disease.
No one can make the decision for you, but I think on your situation, I'd go for the vaccine. Although I would be double checking to see if all the other vaccines are safe in pregnancy too.