There is no difference between 2-part harmony and 2-part counterpoint; counterpoint may be regarded as the melodic aspect of it, or the degree of independence in movement and rhythm.

Let me take the opportunity to mention that in our kind of music, the bass line is the first "counterpoint" (Latin: contrapunctus bassus), therefore it should be treated with more care than most folkies do. Make it a good melody whenever possible, even if you only have a guitar for accompaniment. Afterwards you may proceed to higher voices.

To be sure: Counterpoint, like most music, was invented by folk musicians, the academics only gave it some polish specific to educated occasions. Make sure you know the most important rules, and if you break them in your writing, do so by artistic choice.

sfmans: witness the medieval church's abhorrence of the perfect 4th for example - are you sure you're not confusing it with the tritone?