What do enemies mean when they shout 'plough the lily'?

Solution 1:

Lily refers to Temeria in this case. At the beginning of the Witcher 2 you're fighting for Temeria. The emblem for Temeria are silver lilies on black background:

Ploughing does refer to what you're suspecting, "plough the lily" means pretty much "fuck Temeria".

The Witcher Wiki also explains this particular phrase in the trivia section:

The term "Lilies" is used as a collective noun, likely meant to be derogatory, referring to the people from Temeria. A common phrase used by non-Temerian NPC enemies in The Witcher 2 is, "Plough the lilies!" The term most likely originates from the silver lilies in Temeria's emblem.