So why should some clerk lose their job for acknowledging that , under Spanish law (but not Catholic law), two men be married.
Because it's giving state approbation to an objectively immoral situation, and making it equal in the eyes of the state to a covenant ordained by God and nature.
The Catholic Church doesn't recognize civil marriage anyway. In the Catholic Church's eyes, if you ain't married according to Catholic rite, you ain't married.
Untrue in general. It's true that a Catholic who marries in a non-Catholic rite without a Church dispensation is contracting a marriage which is invalid in the eyes of the Church. Non-Catholics are not required to do so, however, and if they are baptized Christians, their marriages are considered to be just as sacramental and binding as a Catholic marriage. If they aren't Christians, their marriage is considered to be a "natural marriage", which is not indissoluble, but not invalid either.
Incorrect. I suggest you actually learn what the Catholic Church teaches prior to commenting on said teachings.