Q:

Can you walk through rooms with aliens? 

Being in a room with an alien prevents you from walking out, but can you walk through a room with an alien as a 2 room move originating from a room that didn't have an alien? 

A:

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.