Of course the flash would spread over several years until reaching an other system.
But if it's possible, the flash would just be a cool visiual effect.
Technically, I think, the way you see the supernova in-mission is wrong too. Since the star's explosion probably wouldn't travel at light speed, you wouldn't see anything until the explosion got significantly close to your position in-system. However, seeing as it was a countdown of about a minute, it must have been going pretty fast, or you were very close to Capella. If the latter is false it must have been going at light speed or faster to get to you in that length of time. (And Capella's bigger than Sol.)
For example if someone sent Sol supernova (which has already been done:
here) you wouldn't see the flash until a few minutes after the start of the nova, since light takes eight minutes to get from the Sun to Earth. (I'm assuming the explosion/shockwave goes near light speed.)