Relax. It has happened before and with little consequence. The armed services committees have an astounding record of getting a bill enacted every year for 53 years. Along the way, however, there have been four vetoes [1978, 1988, 1996, and 2007]. In each case, the committees fairly promptly -- usually about 6 weeks -- introduced measures without the offending sections and got them passed and signed by the president. Details in this CRS report :http://www.fas.org/sgp/crs/
That means an Obama veto might lead to a failed override attempt, but more likely the committees will just admit defeat and start over with a revised bill. The members have a stronger incentive to maintain their record of successful enactments than leaving their 1,951 page bill and report in the trash can.