You could always put something in dialogue instructing the player to wait till it opens. They won't really be required to, but for the sake of immersion...
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You can use one of the gateway props tied with triggers; there is a blue one (forget which) that looks pretty good for this. I made a DS9 map once that I ended up not using. I had the player dock with the one of the station's upper pylons and put the effect close by to seem large while having the player engaged in a maneuver at an exact point so they didn't go near it to dispel the forced perspective illusion.
*There was a small reach marker at the pylon for the player to dock with the station and a larger one surrounding it.
*The player is directed to go to the pylon (inner reach marker)
*As the player crosses the outer marker, the effect is triggered to make it look like the wormhole has opened.
*Once the player reaches the inner marker to dock, the effect goes away through a second trigger to appear as though the wormhole has closed.
Looked pretty good to me so you can give something like that a try.