In the context of this novel "especially if it means that" means "especially if _what we think is best for us_ means _our extinction_ ". "Extinction" may seem a strange choice of words because we are used to encountering in the context of species becoming extinct. But "extinction" can also mean annihilation.
In the immediate context, "annihilation" makes sense. A few lines later, we encounter the following statement:
> But in any case, an angel of the Lord appeared to Etherius, instructing him to meet Ursula in Cologne, where they would meet glorious martyrdom together.
In other words, for Etherius "what we think is best for us" refers to meeting Ursula in Cologne, and dying as a martyr meant his "extinction".