In some sense, writing strict species counterpoint in a modern "minor key" is an anachronism.
Really, you ought to use one of the 8 Church Tones which were based on the medieval plainsong modes - some of them transposed, and written with modern-looking key signatures of one or two flats, but not conceptually the same as the modern ideas of "D minor" or "G minor". This system was more or less standardized across Europe in the Renaissance and Baroque periods, and is what Couperin meant when the title of a piece mentions the first to eighth "Ton," the Spanish composers by "Tono," etc.
The tonality of this music was not so sharply defined as in the classical era - it would be more accurate to say the music used any of the "well tuned" chords in meantone temperament, and "modulation between different keys" was not recognized as a concept - successive cadences were often in what appear to be different "keys" but the "modulations" don't have much structural function in defining the form of the complete piece.
This little history lesson doesn't entirely answer your questions, because the "leading note" of the "Ton" was often (but not always!) sharpened to be a semitone below the tonic, especially at cadences. On the other hand, for music that was not strictly contrapuntal or liturgical, Renaissance keyboard composers were quite happy to write F# and G# in one hand simultaneously with F and G natural in the other, in the key of "A minor," especially if the notes were separated by 2 octaves - though writing like that probably won't get you good marks in a 21st-century examination! (Meantone temperament softens the effect compared with modern equal temperament, and the resulting clashes don't sound like "discords" at all once you get used to them.)
Another way to approach this question is to stick to the notes that were "in tune" in Meantone temperament - i.e. C C# D Eb F F# G G# A Bb B in the normal tuning with key signatures of 1 of 2 flats - though sometimes G# was retuned to Ab if the tonality ventured somewhere close to the modern C minor.
Here's a brief history lesson: http://www.kholopov.ru/arc/atcherson.pdf