More than 50 stations affiliated with ABC, NBC and CBS have scheduled a syndicated program, the two-hour premiere of ''Star Trek: The Next Generation,'' during prime time this week.

Most of the stations are pre-empting their network series only once to give Paramount's spaceship Enterprise and its new crew a first-time liftoff into the 24th century. However, ABC is permanently losing nine stations, including Boston's WCBV, from 8 to 9 P.M. on Saturdays.

The new Enterprise, captained by Patrick Stewart with a crew of female psychics, blind seers and androids, is replacing ABC's ''Once a Hero,'' a situation comedy about a comic-book hero's adventures in the real world. The debut episode of ''Hero'' last week came up at the bottom of the Neilsen ratings, with a 3.7.

''We chose that time deliberately after we saw 'Once a Hero' last June,'' said Mike Seagly, program manager for WZZM in Grand Rapids, Mich. '' 'Once a Hero' is gone. It's kind of bad for ABC, but we all have to survive somehow, and ABC isn't helping us in that time period. It's possible the network will replace 'Once a Hero' with something better, but I think 'Star Trek' has the potential to perform as well as anything ABC has in development.'' Ball and Burstyn Replaced