Teensy 3.0 Problems with moderate range (~40m) OneWire Signals
The application note you linked to has the following paragraph on page 8, which is in complete agreement with your experience so far.


  Simple microcontroller port pin interfaces are not capable of the
  drive currents necessary to support large- or even medium-sized
  networks. The pullup resistor value is often limited by the port pin
  pulldown capability to around 2,200&Omega;, which precludes heavy
  networks (networks with high weight values). Port-pin-only interfaces
  should be limited to networks with a tabletop radius and weight, about
  3m maximum. (See Appendix A.)


I think that the basic problem is that a "bare" microcontroller pin simply doesn't have the drive strength to create a high-to-low edge on the bus with the timing that the protocol requires. You're going to have to use some sort of master-side driver to make this work.