I feel like -logy and -nomy are more pertinent here, with the -ists being secondary developments from those.
-logy goes back to -λογία, which is a combination of λέγω 'to speak; to collect', λόγος 'word; reason; ratio; ...', or -λογέω 'to speak' (a variant of λέγω appearing only in compounds) and the suffix -ία, which forms abstract nouns. All of these reflect the same root, but it's valuable to distinguish them: while ἀστρολογία 'astrology' is certainly the kind of word we want to look at, ἀνθολογία 'the act of gathering flowers' presumably is not.
Going through the LSJ and filtering out the formations that aren't relevant, we find:
- ἀναισθησιολογία 'insensibility theory' (ἀναίσθησις 'insensibility')
- ἀνδρολογία 'study of men' (ἀνήρ 'man')
- ἀρχαιολογία 'antiquarian lore' (ἀρχαῖος 'ancient')
- ἀστρολογία 'astronomy (!)' (ἄστρον 'star')
- ἐτυμολογία 'etymology' (ἔτυμος 'true')
- φυσιολογία 'inquiring into natural causes and phenomena' (φύσις 'origin, nature')
- γενεαλογία 'tracing a pedigree' (γενεά 'descent')
- γενεθλιαλογία 'casting of nativities, astrology' (γενέθλια 'birthday')
- ἠθολογία 'painting of character' (ἦθος 'character')
- ἰατρολογία 'study of medicine' (ἰατρός 'physician')
- μετεωρολογία 'meteorology' (μετέωρος 'on high')
- μετρολογία 'study of ratios' (μέτρον 'measure')
- παθολογία 'study of the passions' (πάθος 'suffering')
- θεολογία 'science of things divine' (θεός 'god')
- τεχνολογία 'systematic treatment' (τέχνη 'craft')
(That's 15 out of 166 results; this was a varied and popular construction. Note that e.g. βοτανολογία isn't 'botany', but rather 'weeding' (lit. 'gathering grass').)
-nomy goes back to -νομία, combining the same suffix with a form of νέμω 'to distribute, deal out; to pasture' or νόμος 'custom, law', again producing a lot of forms that aren't relevant.
In my view, the relevant ones in the (far shorter) list are:
- ἀστρονομία 'astronomy' (ἄστρον 'star')
- οἰκονομία 'management of a household' (οἶκος 'house')
- παιδονομία 'education of children' (παῖς 'child')
The only form in both lists is ἀστρονομία/ἀστρολογία, but both are glossed as 'astronomy'. There presumably was a subtle difference between these words in principle, with ἀστρολογία denoting the study of the stars and ἀστρονομία merely reflecting how the gods have laid them out, but in practice they were used interchangeably, with ἀστρολογία seeming to be the more popular of the two by a slight margin.
Both words were borrowed into Latin (as astrologia and astronomia), and apparently it's St. Jerome who first made the modern distinction between the two in his Dialogus adversus Pelagianos, in the 5th century CE.
οἰκονομία, for its part, gave rise to economy, and all of our other -nomies are modelled on it: the modern distinction between -logy and -nomy isn't generally one of superstition versus science, but of abstract versus practical, which is a connotation very much built into οἰκονομία. (Though often the distinction is just "this word was already taken as a -logy", obviously.)
So yes, -logy and -nomy both came from Greek, but no, there was no meaningful systematic alternation between them the way there is in modern English. Our zoo of -logies and (especially) -nomies is a modern creation.