For the DUE, at the beginning of your sketch, when using SCL1 / SDA1, you will have :
#include <Wire.h>
#define Wire Wire1
This will replace everywhere Wire by Wire1.
Unlike SDA/SCL, SDA1/SCL1 have no pull-ups. 2K2 as pull-up resistors connected to 3.3V would suffice.
Note that Sam3x I2C has no glitch filtering. It seems the answer is to use a fast-mode compliant isolator like the PCA9517A. The isolator filters 50ns glitches and increases fall time.