Wouldn't the best way to harass trade routes be to attack the outpost and wipe them out?
Only if the outpost isn't defended, or if you have the forces to take it. And that still leaves the 'problem' of having outposts that can be completely disconnected from you empire, but still contributing to it somehow.
If you are worried about realism, this is a fantasy game. If you are worried about lore, the goods are either delivered by a third party merchant guild or teleported, whichever is cheapest for that location.
It's not about realism for realism's sake. It is about immersion. To me it doesn't really feel like I'm building a new civilization from the wastelands if there is somehow a completely functioning trade network already there that can magically transport goods all over the planet.
I feel little need for any connection to an outpost because there is also no connection between cities. Why would an outpost need something that a city doesn't?
If you are worried about gameplay, the current mechanics are better than anything else suggested here.
You must be playing the beta then, if you can speak with such authority about how the game works and if it's any good...