in update notes is listed specifically a continuation of the "join us" organization.  i assume its a pro  sexbot revolutionary group. in my playthrough i'm like day 60 and reached the "Best" church end with shanice, priest bot, and the mysterious warehouse where currently the story content ends. I remember when i came across the organization email i chose not to join them. because it looked sketchy. Should i restart the entire game when it updates to join them or what? Or will the story I am on continue regardless?

Yes. That storyline requires you to join them. 

Don't worry. There's a bunch of other things in this update though.