Can you walk through rooms with aliens?
No you can't as the allowed actions that you can do are not based just on your starting or ending location. As soon as you enter a room with a hostile alien you will be limited to either killing it or using the teleporter to leave that room.

If you look at the action card it only lists kill a hostile alien in your location as an action

English Rules


  Move up top 2 spaces (can do when injured)  
  
  Kill a hostile alien in your location (can do when injured, must do when a hostile alien is present)  
  
  Cary another player 1 space  
  
  Give a skill or tool to another player in your location  
  
  Take a skill or tool from another player in your loctation


If you look at the teleporter card it shows that it can be used remotly, while injured or while a hostile alien is present.