Many of your favorite Pathfinder deities are still openly worshipped in Starfinder. Some have changed since the time before the Gap, and a character might be viewed with unusual curiosity or suspicion for their outdated views. Most deities still accept these followers, and if they're powerful clerics or the like, a god might even send guides to help their faithful find their way home. For example,
Zon-Shelyn still cherishes those followers who refuse to acknowledge their fusion, appearing in their separate forms when answering their prayers. Many deities also have updated their repertoire with tech weapons but still accept followers who use the ancient armaments of their church. Characters who gain proficiency in their deity's favored weapon should choose one or the other. So, a cleric of
Besmara can choose to be trained in the
breaching gun or the
rapier, but not both. Once they do, this decision can only be changed by retraining, and any feats or spells that specify having to use a deity's favored weapon must select one or the other. For an adventure featuring a party that splits their time between eras, you might allow a character to swap their proficiency depending on the time period.