It really changes from school to school, and certainly across regions.
Just for example, I studied and taught at Carnegie Mellon (top-4 in the US), and Java was prevalent. My alma mater is the Technion in Israel, and we did C/C++ the entire way. Folks studying information systems at the Technion, on the other hand, started with Java.
Here's the real situation:
The choices that schools make depend on equipment, incentives from manufacturers, market conditions, and tradition.
Let's start with equipment / software and incentives
Java is free and the popular IDE (Eclipse) is free (and used to be pushed by IBM), and the equipment is cheap (Any old Linux machine would do). Now Oracle is pushing Java again along with its DB solutions.
Microsoft is pushing C# and XBLA and all that stuff so they offer universities cheap site licenses to Windows and Visual Studio to make C# more popular. Don't underestimate the willingness of a school to switch vendors because of a free MSDN license. I also think that Microsoft is offering additional incentives to the schools to use Visual Studio such as scholarships and some faculty awards. On the other hand, many students now have Macs without Windows licenses, so that causes problem for VS adoption since many students want to work from their rooms.
Many of the older languages (VB6, Pascal) use outdated compilers or environments that don't work on most student's machines or require too much installation. For the life of me I have no idea where one would get a site license to Turbo Pascal today if it even exists. I'm sure many high schools with old computer labs use these languages because they can't run anything newer. Universities, in general, tend to have better labs and more updated languages.
Many of the newer languages (like Python) and older languages (like C), don't have a single IDE. This creates a huge problem for instructors since students always manage to dig up all the incompatibilities nobody knew about. Forcing everyone to use the same IDE makes things simpler.
PHP getting dropped is not a surprise - I can't imagine deploying and testing student programs and the security holes this could cause. Also, I'm not sure how one automatically tests PHP programs. There is also a market "perception" of PHP as not a serious enough language. I don't want to start a flame war about whether it is true or not, but we all know that this camp exists.
Market conditions vary from state to state. I think most companies today use VM or "far from the wire" based languages (like Java/C#/Scripting languages). However, many companies that do need "the wire" use C/C++/ASM. In areas near large defense/aeronautics/semi companies, you will see more schools teaching these languages. For example, my alma mater taught primarily C and C++ and still does because Intel and other EE-related companies were major employers and much of the faculty came from there.
Beyond all this, many CS departments make languages choices based on where they evolved from. As a rule of thumb, departments that came out of Math tend to first teach languages like LISP/Fortran/Python/ML. Departments that came out of Electrical Engineering or Computer Engineering tend to first teach low level languages like C/C++. Freshly formed or departments or departments with a heavy software engineering focus will tend to be Java/C#.
As for the actual article: I have to admit that I am really surprised that the educational system in the UK allows high-school curriculum to have such a variance in languages. Usually state boards are more restrictive and try to obtain a uniform curriculum country-wide. I am willing to bet that some of the concern had to be with what the teachers know. If many college graduates don't know C, then many new teachers will not know it either, etc. The goal of high-school curriculum is to teach fundamental CS concepts. We studied in Pascal (back in the early 90s) and that was good enough. Most of our curriculum focused on pointers and data structures, I'm surprised one can even pull them off in some of the "recommended languages".