SilverWook said:

That scene has bugged me since 1979. (Not to mention being totally freaky.) There has to be a easier way to dispatch Ripley than shove a magazine down her throat. And it sure isn't going to look like an accident, or the Alien. Was this supposed to emphasize Ash's major malfunction?

Pretty much. Either in the commentary or the making of Scott mentions that he was going for freaky and sexual (the magazine bit) with the scene. The malfunctioning android's idea of sexual intercourse, or something to that effect.