In theory, you can re-use the JTAG pins on a SAM3 as GPIO - PB28 to PB31.
The SAM3X8 datasheet says:
SWJ-DP pins can be used as standard I/Os to provide users with more general input/output pins when the debug port is not needed in the end application. Mode selection between SWJ-DP mode (System IO mode) and general IO mode is performed through the AHB Matrix Special Function Registers (MATRIX_SFR). Configuration of the pad for pull-up, triggers, debouncing and glitch filters is possible regardless of the mode.
But I can't see anywhere in either the datasheet or .h files where MATRIX_SFR is ever mentioned again (nor any other hints on switching the pins to GPIO mode...)