It's not a big problem, you're absolutely right. But, it's an unnecessary annoyance in it's current form is all.
Other then saying I don't feel that Sector Space should be a safe haven like a Starbase there's not much more I can say about the issue. The threats to the player just can't be in the missions you go to, IMO. That doesn't mean I don't think DSEs can't be better: you should never zone into a death squad, but I do think they add a sense of drama to the game, especially when you have to fly across 3 zones to get somewhere.