I am actually wondering about this now too. However a couple issues. Loki was left my Laufey to die because he is too small, Odin says so. So more likely his mother isn't terrain (human) but could've had the same form and been from another planet. We see many human looking people not of earth. Whoever it was- if she was human or mortal she died a very long time ago.
This is one of the best lines in Iron Man 3 because Tony knows that being in a relationship with Pepper puts her in harm's way, but he loves her enough to keep her safe above anyone else. Maybe being in a relationship with Iron Man isn't so bad after all. ;)