is it permissible to use lower case for the Latin names of plant diseases in the body of a text? (The cases in point here are 'sclerotinia' and 'phoma')
The two examples you give are actually the genus part of the scientific names of the plant pathogens. Usually these are capitalized when they appear in genus-species nomenclature. The genus lends it name to the disease itself, and what you want to know is whether you should capitalize the genus when it names the disease. Alas, there appears to be no rule valid across publications. The Farmers' Bulletin (Issue 1184, 1953) capitalizes the name as the genus of a fungus, but not as the name of the rot caused by the fungus:
Two gensing diseases are caused by fungi of the genus Sclerotinia. The diseases are sclerotinia white rot, and sclerotinia black rot.
Australasian Plant Disease Notes (2006) opts to keep the name capitalized in both uses:
Symptoms exhibited were watery brown, irregular-shaped necrotic lesions ..., which are typical of Sclerotinia white rot recorded on other hosts....
Here, the genus name is incorporated as such in the disease name. (You can tell because it's italicized.) So it makes sense that it's also capitalized. However, the USDA Research Service in a 2011 publication capitalizes then name of the disease in all roman type:
Examples would be apple scab [Venturia inaequalis (Cooke) G. Winter], Sclerotinia white rot of canola and beans [Sclerotinia sclerotiorum (Lib.) de Bary]....
This is clearly a style issue that will be decided by the publication which has engaged you. Your best bet is to consult the publication's style guide or your editor.
(Emphasis above is mine.)