What about Panama Canal system, or Suez Canal system, or St. Lawrence Seaway system? What about 'Huge Chunk of the Pacific Ocean between Hawai'i and California' system? I can think of many cases where two empires basically form an 'X' through a starless nexus, crappy little red dwarf, or 'interesting space terrain' system and don't want the other one to colonize or build bases there, but recognize their right to pass from A to C.
Yeah, I think the concept of an open borders treaty is the right fix here(conditional, as always, on Steve's free time), which is why a lot of 4X games do things that way.
In a perfect world, I'd also love to set up trade orders at particular colonies, to be fulfilled by nations I have trade treaties with (i.e., open borders for civilian ships only, or maybe civilian+commercial), in exchange for Wealth, not just my own civilians.