A micro-organism is literally what it says – a very small organism. Bacteria constitute a big group but amoeba like organisms and fungal cells are also very small and qualify. Viruses are not living organisms in the same sense but they are often referred to by this term.
A pathogen is, by derivation from the terms "pathogenic" and "pathogenesis", simply "a disease causing agent". So asbestos is a pathogen much as is the tuberculosis bacterium. Unfortunately, there has been a sloppy drift due to the mass action of common usage and this has led to "pathogen" being used initially as an abbreviation for – but then being used as a "legitimate" synonym for – a pathogenic (micro)organism. This continuing drift is apparent in various dictionary definitions. This trend, where pathogen is "highjacked" to be – exclusively – a pathogenic micro-organism, is well under way in about half the current dictionary definitions.
It is helpful to remember that most cellular micro-organisms (eg, bacteria, fungal cells, amoeboid cells) patiently wait for other life forms to die before they recycle their corpses back into the ecosystem; and they perform a critical function here. Pathogenic micro-organisms represent but a small fraction (no more than 0.1% of all micro-organism species) that cheat. They have evolved mechanisms to damage cells and provoke debris to help them thrive whilst the host is still living. They are indeed "pathogens" – that is, agents that damage cells/tissues – but the word should not mean more than "an (unspecified) agent that causes disease"; particularly, if the general use of pathogenic (disease causing) and pathogenesis (the mechanism of disease production) are not themselves to be corrupted into a restricted meaning that deals only with micro-organisms.
I am not surprised you are confused – I think most bacteriologists and immunologists confuse themselves with this constricted interpretation of "pathogen". They flit between pathogen and micro-organism with hardly a thought for the distinguishing properties. It allows them to be imprecise.
There is an article about this in the August 2008 edition of the Scandinavian Journal of Immunology.
