Are there specific non-protein substances that pathogens release into their host?
Sticking my neck out (and expecting it to be bitten by a black swan) it appears that all the examples of toxins secreted by bacterial pathogens when they infect an animal host (exotoxins) are proteins. 

However fungi secrete a variety of exotic (and often very nasty) small non-protein molecules (mycotoxins). It’s not clear from the question whether you would be interested in these systems as they differ somewhat from those involving bacteria. One difference from bacterial toxins is that fungal toxins not secreted inside an infected cell, but just into their environment. Thus, cercosporin is secreted onto the surface of plants on which Cercospora reside and may be taken up through lesions in the plant. However it is not clear whether the plant is the main target of such toxins, rather than bacterial ‘foes’. So the host/pathogen concept is less clear in this context.

A similarly ambiguous host/pathogen situation would appear to exists with toxins such as saxitoxin, the paralytic shellfish toxin secreted by certain marine algae and cyanobacteria.