I think it's probably at least in part to do with what you said- Programmed Amnesia can be removed, Mindrape can't. There's also the behaviors of the spells themselves. Programmed Amnesia takes a relatively long time to work and, at least relative to Mindrape, gently changes the subject. Mindrape is more "Bam, your brain is now my ****!" Kind of like the difference between attacking somebody with a fireball and attacking somebody with Avasculate; one is a much nastier, painful (and more effective) experience.