Dictionaries, it is said, record how our language is used, but are then used as a reference for how it should be used - i.e. what "correct" meanings and usages are.
How should we view the change in usage of the verb "substitute", which is now very commonly used where we used to use "replace"?

E.g. "..pupils are not allowed to use these [unspecific] words... but substitute them for a specific term."

My view is that it would be better to say "a specific term should be substituted for the banned word", or "the banned word should be replaced by a specific term", and the user is contradicting himself by apparently suggesting that the banned word be used instead of the specific term.
It is also not uncommon to see or hear such mixed usages as "substitute them by a specific term" where one word is used with the preposition appropriate to the other.

So - back to the question: should we be worried that one term is replacing another whose previous usage was opposite in sense (at least as far as direct and indirect object are concerned)?
It's happened before (e.g. presently and immediately).

As the quotation I first gave as an example was published in an educational magazine and written by a teacher (of geography), is there any hope of doing anything about it?
SpudUK.

Hey, Spud, welcome! :-)

is there any hope of doing anything about it?
Now that, I dunno; but I can say that I think the sentence you quoted is terrible, for the reasons you stated.

Some time ago, someone here brought up the phrase (I) "graduated high school". At the time, I hadn't heard (read: noticed) that usage, but since then I've heard it all over the place--and it grates on my nerves.

Language changes are sweeping, I guess...including sweeping aside the objections of some folks. There are some who are battling, however, such as The Apostrophe Protection Society. See web page. Maybe you could start a similar group for use of the word substitute!

I would be interested to know whether anyone in the States has seen the word used as our friend from the UK describes. In other words, is it a British-only (mis)usage? I am thinking of an expression at least one Brit-speaking friend uses that always gives me pause: that someone is "meant to do" something, where we would say was supposed to do something.

To me "meant to do" says that the job was something the person wanted to do, but it was not urgent or even important but something that could be taken care of later with no harm done.
On the other hand, "supposed to" says the job was required, and was not done and the lack of action is regretable.

And it bothers me that "presently" is often used now to mean at present or currently. In the older dictionaries I have "presently" means "in a moment" and that was how I was brought up to use it. Seems today's it has changed it to be the same as "at present." Harumph!

The problem seems to be one of "almost synonyms."
You replace thing A by substituting thing B. The general gist is the same; B is where A was. Sloppy grammer doesn't notice the details, that each verb has a different object in the operation. Sloppy logic then states the same general idea = the same meaning = interchangable verbs. (Did I get the grammatical terms right? I was of the generation that didn't study grammer.)

edit Unfortunately

I had to leave my office so they could use it for an interview so I'll finish in a new post from the other room.
To me "I meant to do it" indicates I intended to but didn't regardless of how important the task was although it often preceeds a weak excuse. "She is/was meant to" indicates some kind of cosmic choice, like "it was meant to be". "Meant for" which looks awful in print is used around here to mean "intended" whether or not the intention was fulfilled. "I meant for that to happen."

My friend would say, for ex., 'I was meant to go to the doctor this afternoon, but my car wouldn't start'.

record how our language is used, but are then used as a reference for how it should be used - Why "but"? Language should be used the way it is used, thus attempting to maximise comprehension. "Mutations" of the sort you describe are seldom lethal, i.e. they are unlikely to prevent comprehension. If they fail to provide improvement, they usually disappear with passing fashions.