One of the most easiest methods is to create a teleporter-out. Preferably towards the center of the map in my opinion. Two-way portals are also good, but I'm not entirely sure about a human teleporting into the alien base, nading and teleporting out :O
On the other hand, you can use the very over-used method: Create another hallway entrance to the base.
I just realised this, but alien survivability actually relies on doors heavily for buildings. Will the map have any doors around the alien/both side(s)?
Yes there will be doors. And many of them haha.
Here is a very quick sketch of the alien ship as well as a couple of way points. If you look on the map design you can see that this here has a bridge from the alien ship going into the centre pyramid and a dirt train going beneath the bridge in a pond which is along side the pyramid. Although I am planning on making the pond at the bottom of a slope and test it.