Hmm... Well, the extraterrestrial explanation, even if completely natural sounds like ASB to me. Asteroids are slow, and follow their orbits quite rigidly. With POD after 1650 AD it would be inplausible that it would hit the Earth within hundreds of years.
Ebola forms a localised outbreaks. It disables person too fast for sick to move and spread the disease further out. Another outbreak of Black Death, would be deadly but again, it would be quickly stopped by quarantine. At gun point if necessary.
An epidemy sounds plausible, plague could kill some philosophers or scientists.
Who would be most crucial for further progress?
Spinoza is eighteen, probably didn't made any influence yet.
Leibniz is four. He would be another child dying in his youth.
A plaque that would hit both, is a long shot but remotely plausible. Spinoza lived in Rotterdam. If a plaque started there it could be transported aboard ships to northern Germany.
How would world develop without them?