Add this to your boards.txt and burn the bootloader once. The bootloader is not used, its just to change the fuse. Then you can upload via isp and the sketch will load
## Arduino Mega w/ ATmega2560 Testato Mega ISP Version
## -------------------------
mega.menu.cpu.atmega2560T=ATmega2560 (Testato ISP Version)
mega.menu.cpu.atmega2560T.upload.protocol=wiring
mega.menu.cpu.atmega2560T.upload.maximum_size=258048
mega.menu.cpu.atmega2560T.upload.speed=115200
mega.menu.cpu.atmega2560T.bootloader.high_fuses=0xD9
mega.menu.cpu.atmega2560T.bootloader.extended_fuses=0xFD
mega.menu.cpu.atmega2560T.bootloader.file=stk500v2/stk500boot_v2_mega2560.hex
mega.menu.cpu.atmega2560T.build.mcu=atmega2560
mega.menu.cpu.atmega2560T.build.board=AVR_MEGA2560