I could be wrong, but I seem to recall the only thing he hated about Alien was the fact that it was butchered by the director (bits of his similarly brilliant Freud were interpolated). If you buy the Intrada 2 cd release of Alien you'll get the WHOLE score (minus the interpolations and plus the music that wasn't put into the movie because of Ridley Scott being a dumbass). It was mostly his problems with Scott that ruined his opinion. Really, if you don't have the Intrada release, I can't recommend it strongly enough.Alien.
Yes, it's not necessarily the most hum-able or pretty sounding score he's ever written, or remotely one he considers good, but it's the first film score that I heard that taught me the fundamental lesson that music can make you feel terrified.