I will try to paraphrase (not literally translate) what the quote says:
First sentence: Thesis.
Man isn't as fragile as rose, a self-sufficient being, but even more, so that he can be brought out of his equilibrium by such simple phenomena as vapour or a drop of water, because he has to think about it.
Second sentence: Explication.
He (identified with his thinking!) has to evolve, include every single phenomenon into the framework of his thinking, and therefore his self-conception is always endangered by the universe (read: nature/phenomena) to be challenged and eventually "crushed". Man then has to reinvent himself, the old self is killed, and a new, more noble one, is born. But in the end, it is man how "kills" himself, not nature.
The link out of the comment of @MauroAllegranza pretty much contextualises this historically as I understand (only six years french in school, maybe I got all wrong ;).
Therefore, the violability allegorically expressed in the first sentence is nothing more than the other side of the medal of "Toute notre dignité consiste donc en la pensée." - All our dignity consists therefore in the thinking. - The sentence following your quote within the very same Pensée, leading to a notion of morals. It is our source of nobility to cope with the universe in thinking, always throwing over our obsolete self-understanding.