That's like saying "The problem with teaching people how to drive cars is that at the end, they don't know how to ride motorcycles".
There are plenty of other classes at the grad and undergrad level that teach you about lower level concepts such as pointers and memory (system, C, OS, ...). The Java classes teach different concepts.
I never got C or C++. The OS course, sure, but it was awfully theoretical and we didn't get to code all that much. Depending on the rest of the curriculum you should probably decide what to use to teach introductory CS.
There are plenty of other classes at the grad and undergrad level that teach you about lower level concepts such as pointers and memory (system, C, OS, ...). The Java classes teach different concepts.