What is ironic about the poem is that he is using the mouse as a metaphor for the lower classes, the social strata which is unjustly chased and ran over by the higher classes, and by their governments, and for once, they are being considered worthy of something good.
He wrote the poem metaphorically to demonstrate that, although a mouse is considered a filthy little animal, what exactly makes it so? Why are we to kill it? How much wrong could he do to deserve death? We might feel so much superior only for being human, but aren't humans more destructive, more elitist, and more disgusting at times than a mouse itself? And, for that, do we get killed? No, we even ask for mercy! Yet, the mouse has none..except that given by the protagonist of the poem.
Equally, the middle and lower classes continue to be bombarded by their governments and especially by the higher classes whom (at that time) dominated the world. They treated lower social strata like lesser beings, and did not think they deserve any opportunities for a quality of life. Hence, the author equally gives validity to this axiom and reinstates his position as a person with a quality of mercy for everyone, equally.