I know this is an old topic but in case someone looks at it and needs help I'll post this.
I just glanced at the cpp and h file for software serial on Arduino. The authors made the handle_interrupt function public so all you should need to do is comment out or delete this section of the cpp
then set your interrupts up inside of your code. You can call the software serial interrupt from inside your code. MySerial.handle_interrupt(); or whatever you want to do
I haven't test it but I will in just a second so you will know if that it does work