Alan Baker wrote:
In a glide in a low wing aircraft:

Total aerodynamic force (lift and drag!)
^
|
|
M (Centre of Mass)
|
C (Centre of Aerodynamic Pressure)
|
|
Weight (no down arrow head... ...sorry)

Now remember, the aircraft must be descending to make this work.

The above diagram is simplified too soon in the analysis. You may as well
have dispensed with the weight and aerodynamic forces too, as they
contribute nothing to your subsequent argument since you never vary them.

Now if you add thrust at the "drag line" (the line through the CoP
parallel to the aircraft's motion):

Total aerodynamic force
^
|
|
M (Centre of Mass)
|
(Thrust)--C (Centre of Aerodynamic pressure)
|
|
Weight

You can align the engine any way you want and it will still create a
pitch up, right?

Sure - and the object will rotate about M until it reaches a rotation
speed in equilibrium with air drag (by definition, the only point where
we are allowed to add that drag component is at point C):

Total aerodynamic force
^
|
|
M (Centre of Mass)
|
(Thrust)--C--(air drag) (Centre of Aerodynamic pressure)
|
|
Weight


But:

Total aerodynamic force
^
|
|
(Thrust)--M (Centre of Mass)
|
C (Centre of Aerodynamic Pressure)
|
|
Weight

Add the thrust at the centre of mass, and you get no pitching moment.

The diagram above is of a system that isn't in equilibrium. Furthermore,
there is no vector we can anchor at C that brings it into equilibrium -
if we add a vector so that we get a pure couple, like so:

Total aerodynamic force
^
|
|
(Thrust)--M (Centre of Mass)
|
C--(air drag) (Centre of Aerodynamic Pressure)
|
|
Weight

....then the _couple_ rotates the aircraft around M in a counterclockwise
direction (i.e. pitch down!) Your force diagram is flawed because it
makes incorrect assumptions about the location of C at equilibrium and
the direction of the total aerodynamic forces.

Running the thrust line through M does _not_ guarantee you wont get any
couple.

In fact none of the diagrams you or I drew are complete and do not
accurately capture the reality. Center of mass changes with each flight
and even during flight, and center of pressure changes with aircraft
orientation.