Watchdog in Arduino Library - or at least support by bootloader

I am having mega 2560 board with "bad" bootloader. I am asking myself, if I can solve the problem with non-disabled watchdog by bootloader with this trick?
Can I add "wdt_disable();" before a "wdt_enable (WDTO_8S);" in a void setup (WDT will be set to 4 or 8s to ensure that bootloader will load completely)?. Will this trick do the job?