"n'en est pas moins" is a construction which means something is surprising if we refer to what we know of the context. "Il sait que fumer est mauvais pour lui, il n'en continue pas moins à acheter des cigarettes." "He knows smoking is bad for him, yet he keeps on buying cigarettes." So it is (more or less) an equivalent to "yet", I think. "en" refers to the context of the sentence, it links to the reasons which explain why this decision (destroy the Bastille) is surprising.