the ship would usually end up near the Witchspace Point again because that's the "weak spot" to come out of Witch Space in the system.
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odds are high that you will end up well off the normal routes, which means that you are much less likely to be attacked en route to the station.
In regards to that, would it be possible to create alternate wichspace points? I'm not sure it'd be possible for current game mechanics to jump you into a system that's anywhere but the WP beacon, and anyways that's not quite the point of the OXP. But once you're in system, if you use the Probability Drive, it could potentially wind up teleporting you to an alternate witchspace point. And to clarify, by that I don't mean an entirely new jumping point for the system. Just a beacon/waypoint, with several ships spawned in, to give the appearance of it being an alternate jump point. Here's some ideas, if you're interested.
Police beacon - Obviously the best place to wind up, (unless you were just in a fight with Galcop!) it's a beacon swarming with Galcop or other system vessels. Galcop would need their own beacons in certain systems, due to the large amount of priority traffic. It keeps the lanes uncluttered. (And explains the lack of police in the main trade routes....)
Military beacon - Could either be good or bad. Large and powerful ships probably would disturb some of the more loony people in the galaxy, and invite challenge, so the military likes to keep it low-key and away from the general public. That translates into either they'd not care, or they'd become very hostile if you saw something "top secret."
Pirate beacon - Obviously very bad, unless you yourself are a criminal fleeing justice. Pirates would need their own beacon, due to the random chance of a patrol hanging out around the WP beacon. Could also end up being next to a rock hermit or asteroid field, way out of the main space lanes.
Trader Guild beacon - Large cargo haulers and their respective escorts. Major companies may have secret jump points installed so that they can ferry lucrative deals in and out with realitive ease, and maybe deal in the more shady aspects of marketing. Could be hostile or friendly depending on the player's legal status.
Thargoid beacon - Nobody wants to wind up here. Large bounty if you manage to blow one up, though.
For these to work, it'd need to be well outside the normal scope of the spacelanes. Probably an equal if not greater distance from the planet as the regular WP beacon, and it'd make sense to be farther away to attract less attention.
I think another idea (sorry, slapping on all these suggestions that may be way out of the scope of the OXP) for realism or to make it less game-breaking, is to have a potential for ships (or missiles!) in a certain radius to be teleported with you. Sort of like a wormhole, except it doesn't linger. This also translates into the player ship - If an NCP carries this, and teleports out, then you might be taken with him. But of course the NPCs could purposefully teleport to a beacon or pirate cove or somewhere where they'd have backup, so it'd be very dangerous to wind up getting caught in their drive.
I like this idea though, and I'd be sure to download it if you came out with a release version.