This should be an absolutely painless transition for almost everyone.
Virtually all Arduino programming is done in C++.
They call it "Wiring" but that's just:
- a standard library that provides interface functions and symbolic constants for the I/O pins, timers, USB etc
- a preprocessor that adds a #include for the library header and prototypes for all your functions so you don't have to care about the order
- a driver main() that calls setup() and then repeatedly calls loop()
- the avr-gcc c++ compiler
You already have to select which board you are compiling for from a menu. Different boards are using different AVR chips with varying MHz, varying amounts of flash and RAM and EEPROM, and different constants for the I/O devices. The ARM chip just has more and faster of everything.
There will be an "Arduino Due" item in the "Board" menu which as well as the normal selection of the appropriate library header file will select the arm-gcc compiler instead of the avr-gcc compiler.
No ordinary end-users are likely to have written anything in AVR assembler. 99.9% of everything will Just Work.