It's an issue of gameplay and story segregation, yes, but since they integrated the respawn points into the game world itself it doesn't work that way.
Seriously, they should have just had you pop back into existence at the start of the area. Maybe make checkpoints glowing balls of light or something. In those cases, it's easy to mark it off as 'oh, I'm the player, of course that's going to happen' but with respawn points? Recorded messages from the company talking to as you respawn? Yet for some reason the player characters are the only ones who can ever use them and they're never mentioned by other people? Sorry, WSoD can only go so far.
I actually kinda liked the respawn stations, but you're right it doesn't hold up to examination. We suspected that the stations are mainly used by the bandits, explaining their entirely absurd numbers and making Pandora less of a money sink for Hyperion.
We decided that maybe Hyperion is just so profit driven that reincarnating the heroes was considered a profitable action. Assuming the respawning process is cheap to run, they can make money off the dead hero *and* all the bandits (or Hyperion employees) who need the service.
Of course, eventually Jack really wants to kill the heroes... But can't. He even
Pays them to humiliate themselves by committing suicide off a cliff
but never disables their respawn privileges. Any explanation is a bit of a stretch, but I like to think that it's an intricate bureaucratic process which takes months to go into effect. It involves turning down profit, after all. So the original heroes are banned, and maybe other citizens of Sanctuary, but not the current PCs.
As for Jack... It was done behind his back. He doesn't exactly treat his employees well.
(I've barely played the pre-sequel, so I dunno if it contradicts my longshot theorycrafting)