Listen to your conscience
It is these small incidents that actually test the integrity of our choices. It is easy to say that I love plants, animals and nature, but difficult to practically potray our feelings if we think that may make me look like a harsh person. Decide what you really want to do. Live with neighbours who might one day get tired of all the trees in the neighborhood becasue of the foliage they have to clean or the squirrels, birds etc. living in it or leave a good tree all by itself that is providing nourishment to the squirrels, making your yard look greener, providing shade, and not to forget the oxygen you and the neighbors breathe.
Do stick to the decision once made.