Remember the Four Forces? weight ahead of lift, thrust below drag.
Only weight need be at centre of mass.

See http://www.myaeromodelling.com/wp/wp...mic-force2.jpg

Thrust below centre of mass will have an effect ONLY during
acceleration by the propeller, or decelleration if it has enough drag.
The rotational couple will be much smaller than that caused by the
thrust/drag or lift/weight offsets, and pitch changes are largely due
to the propwash over the stabilizer anyway.

There have been numerous airplanes built with low thrust lines.
Lemme See:

The deHavilland Dragon Rapide:
http://www.deltaaviation.co.uk/gifs/..._Airbourne.jpg

The deHavilland Cirrus Moth: http://www.apda61.dsl.pipex.com/Av12/G-EBLV.jpg

Curtiss R: http://www.aviationhalloffamewiscons..._curtissR6.jpg

The Lincoln Standard: http://cdn-www.airliners.net/aviatio.../7/0817761.jpg

Koohoven FK-41: http://www.henrikaper.nl/koolhoven-f...q-sunlight.jpg

I don't see any of those engines perceptibly angled up or down. They
fly just fine. The original Knight Twister used an upright inline
engine, with the resultant low thrust line, and also flew well.

Having a lower thrust line will pull the nose up more. Decreasing the
stab incidence a tiny bit will fix it.

Dan