The use of “alien” for foreigner in official US parlance has always struck me as odd, and I remember it from the mid 60s when I first heard it on TV in the form of a televised reminder to all “aliens” to register annually at a local post office by 1st each year. In SiFi, “alien” replaces the Greek, barbarian, for non-Roman citizen / non-Earth human.
Some SiFi writers – Clarke for instance – explore more exotic forms of alien life. How aliens are depicted depends on the type of role they play in the story. When they interact with humans in a significant way, they are generally depicted as human or human-like. This is common in the various iterations of Star Trek, though that may have been due, in part, to technical limitations of the times (late 60s), and to budget constraints. More exotic aliens appear in Star Wars about ten years later, with a bigger budget and improved technology as well as a different message.
I don’t see discrimination embedded in this. If anything, the genre allows us to suspend normal rules and expectations and imagine a different world, where appearances and origins are not important.