apple id

And it's 9.3.1 that you've updated to, not iOS 9.3 (If you can't activate your iPhone, iPad, or iPod touch after installing iOS 9.3 - Apple Support) ?

I you were the original purchaser of the phone (i.e. it wasn’t bought used) then you could try going to an Apple Store (make a Genius Bar appointment if you do) or try contacting iTunes Support online (http://www.apple.com/support/itunes/contact/) and see if they can remove the phone from the account - they are likely to want to see proof of ownership before they might help e.g. original receipt with the serial number on it