It is to be noted that Gesundheit is German for wellness or health, not "God bless you", similar privileges of occurrence though it may have. The word is derived from the adjective gesund, plus the derivative affix -heit (roughly equivalent to the English -hood or -ness) to make it into a noun. Thus, the desire expressed is not for God to keep your soul from flying out your nose, but rather the much more practical wish that you get over the cold that's got you sneezing.
rp: this phenomenon stretches to Spanish, with Salud