For A-level students in the UK, there is only one exam board that runs a real philosophy course. And that's about to be changed into yet another religious education course.

For the last nine years, I have taught the AQA's A-level philosophy course. It's a good course, and the only one to represent the breadth of philosophy as a discipline in its own right. So I was somewhat surprised to learn that the AQA have this week, without warning or consultation, published a completely new draft syllabus, which is now just waiting to be rubber-stamped by Ofqual.

The new specification completely excludes the previous options to study aesthetics, free will, all European philosophy since Kant, and – most significantly – political philosophy. This will be all replaced with a compulsory philosophy of religion topic, which will make up 50% of the AS course.

The exam board will also reduce the marks given for students' ability to critique and construct arguments, and more marks will be given for simply knowing the theories involved. Essentially, where young philosophers were previously rewarded for being able to think for themselves and question the role of government, the new course can only be passed by students who can regurgitate classic defences of the existence and perfection of God.

It would not be difficult to see, were one looking for such things, a rather sinister agenda in all this. Secular students who consider the question of God to be irrelevant to their lives will simply not have any other option if they wish to be philosophers.

Meanwhile, the areas that have been casually dropped are the very areas of philosophy that make it a dynamic, relevant and academically rigorous subject. Political philosophy helps us make sense of politics and consider the importance of freedom and justice; considering free will gives us an opportunity to consider our responsibility for our actions. Both of these are apparently no longer worthy of teaching – nor is the option of a detailed reading of philosophical texts like Plato's Republic or Mill's On Liberty. It is not merely that the course that has been dumbed down; philosophy itself is being misrepresented.

A representative of the exam board told me on the telephone that it was "too difficult" to comparatively assess students across the different topics which were options before, so they were changing it so that everyone had to do the "most popular" ones. This is a bit like a science examiner saying that it would be "too difficult" to assess both physics and biology, so it would be better to just drop physics altogether.

(The reason philosophy of religion questions appear "popular" with students is actually that many centres ill-advisedly get an RE teacher to teach the course. Not being philosophers, they tell their students to do the religious questions whether they like it or not.)

But there is a broader danger than this. Philosophy – the vibrant, engaging, and often controversial practice of subjecting all concepts and ideas to rigorous logical scrutiny – has struggled for many years to be properly understood as a discipline apart from religious studies. And yet, philosophy is absolutely crucial for a proper questioning of the assumptions we make about government and about our lives in general.

In a climate where university philosophy departments face closure, the very survival of philosophy in the UK depends on philosophers being able to make clear to post-16 students what secular philosophy is and why it is worth studying. It is difficult to see how the new specification will make this anything other than impossible.

Not only will future students not get a representative grounding in philosophy; it is likely that schools and colleges will eventually cease to run a discrete philosophy course, and will increasingly staff the course from RE departments – if they run it at all. The implications for the discipline in general are likely to be devastating.