Just to make it clear (and good morning from Germany, my Switzerland neighbor):
You want to use the PFS scenarios without actually playing PFS, correct?
Do you plan on having your players be PFS agents? This would change some answers - the Confirmation, for example, is a great introductory adventure to the society. But it loses quite a bit of its charme (in my opinion) if it's just used as scenario without these connections.
Some scenarios work fine if you start them with "X hired you to do Y" (or something along those lines), while others are quite a bit more interwoven with the society (All those "Your predecessors screwed up, go fix it" scenarios).
It should also be noted that while all PFS characters have to belong to a faction, faction missions are gone from society play. There are sometimes boons in scenarios for members of a certain faction (e.g. "Zarta Dralneen asks Dark Archive members before the scenario to do X"), but it's far more in the background than before.