Yes, this is a real bottleneck. In my own campaign set on post-war Kimanjano this is the key problem - both in the game, for the refugees who just wish to go anywhere else, and for me as a realism-minded GM who can't figure out how you ship 500,000 refugees onto a planet quickly.
Building a smoothly running (and cost efficient) orbit-ground infrastructure will be a major issue for any colony. Beanstalks are clearly worth their price and rotons help, but the orbital station/spaceport system is going to seriously limit how many can come or leave per day. This means that any disruption here can hamper the whole system: colonists being left in orbit in too small spaces, serious economic losses, etc. As soon as a colony has two ways to get up and down things become less pressured.
From my players' perspective this of course mean that to annoy the hated governor-general the most they will strike at the spaceport...
