Hmm, in my view writing operating systems and compilers is also pretty far on the side of "applied CS" right around building websites and smartphone apps. But this doesn't strike me as a problem unless people are really confused and choosing CS programs in order to get experience building websites. From what I saw when I was in college a decade ago, even most of the smaller schools were starting to have special "Software Engineering" tracts since they recognized the growing popularity (or at least prestige) of programming jobs. I chose CS because I was fascinated with the actual science and math, and I wouldn't recommend anyone with the same fascination to skip theory courses.