After I had spinal surgery I was told BOTH TIMES, that if the exercises caused me pain, I was NOT TO DO THEM. Now, it would seem that it would hold true for you too. I don't see where things would have changed -- I cannot see why they would want you to work THRU the pain. That doesn't make sense, because that just makes the pain worse!
I would talk with your therapist. Ask him/her what to do. If it hurts to do it, are you supposed to STILL do it. I would think not, but ask him.
You don't want to mess up your recovery, that's for sure. I wish you the best. And use ice for pain, 20 minutes every 2 hours. It worked for me!

God bless and please take care. Hugs, Lee