Plenty of people get killed off in sci-fi, even well known and loved characters, for differing reasons.
As for Apophis - the Goa'uld have been fighting amongst themselves for millenia, so he may have been threatened before, but it has generally been by other Goa'uld, or people of no technical capability (relatively) e.g. Egyptians. Or other really advanced races (e.g. Asgard). They seem quite easy to go for peace if inferior (to Asgard AND other Goa'uld) but will probably always plan and plot for getting the better hand (see "The Devil You Know"). Perhaps in most cases the fighting is actually between Jaffa, or between vessels of roughly even capability, and therefore he, personally, is at limited risk. In this case, he was at personal risk.