You're one to talk. None of the three definitions in the link you gave match the one you appear to be using. The first one doesn't apply to porcupines eating branches of your tree - unless you just failed to mention that you're a farmer and your garden is actually an orchard. The second would cover the porcupine - but would also cover the case that you were clearly implying is ridiculous, unless you think rats aren't bothered by you setting up traps.

This is pretty common when people insist on using literal interpretations of dictionary definitions: one might be too narrow in practice, the next might be too broad. The way in which we actually use language is just too nuanced to consistently fit into neat boxes like that, and that's even before we consider what I was actually getting at, which was subtext. The word "pest", when used in actual sentences by actual human beings, clearly has connotations that go beyond a technical agricultural definition. No dictionary is going to tell you the subtext of what a word means in context. It's almost like dictionaries are descriptive, not prescriptive.