I've replaced chips on this scale before, it's do-able but not easy, you have to wonder for the cost and effort is it worth it?
There are so many other things that could have been fried, smt resistors or even the pcb traces, i've not looked that closely at my Mega board to see how many layers it have but it's a pain when one of the hidden layers gets fried.
anyway, desoldering the Mega1280 is easy, as with all smt reworking i do i just flood all the pins with solder and use the iron to heat each side quick then just pick the chip off the board with fine tweezers.