there IS a way out of this... but ive only pulled it off a few times...
order the base to "dock at next base"
dock the ship normally.
once the ship is docked, order the dock to "dock at next base" (do this after all the repairs are done, youll be able to get on the bridge once docked, check brex to make sure repairs are complete)
this SHOULD circumvent the cutscene and let you sit in the dock.... though the doors may end up repositioned, IF YOU DONT DO THIS, you wont be able to warp out of the system, as the game will think you are still docked.
.. i recommend turning off collisions for this..