One might think that the reason for Mordechai’s refusal to bow is the low regard with which the Torah holds worship of anyone or anything outside of H-Shem. According to the Midrash (Esther Rabbah 7:8), however, Mordechai admits that bowing down to a person in-and-of-itself is not wrong. For example, Yaakov and his family bowed seven times to Haman’s ancestor, Eisav (Bireishis 33:3). In fact, Mordechai deflects criticism of his not acting likewise with Eisav’s descendant by citing his ancestry from Benyamin, who had not yet been born during this incident. The Maharal adds that, in reward for this, Benyamin inherited the part of Eretz Yisroel where the Kodesh Kedoshim (Holy of Holies) of the Beis HaMikdash would stand. Mordechai was concerned that bowing to Haman would cause him to lose his connection with the Shechinah (the Divine Presence), just as the Shechinah left the Kodesh Kedoshim when the Jews no longer deserved her.
In Michtav M’Eliyahu, R’ Eliyahu Dessler writes that Mordechai’s defiance can teach us to attack our Yetzer Hara head-on without a kernel of compromise. Any capitulation can lead to a downward spiral of spiritual loss.
The Malbim writes that Mordechai did not bow down to Haman to avoid ascribing divinity to him. In an era when people ascribed godliness to their rulers and the rulers’ courts, Mordechai felt compelled to demonstrate his variance with heaping any possible blandishments of divinity upon Haman.
Rav Eliezer Ashkenazi writes that the command to bow to Haman referred to two different groups of people – regular subjects of the king, and higher-ups sitting at the gates of the king. Mordechai did not fit into either category. As a Jew, he was not a citizen of the realm. At the same time, as an adviser of the king, he sat at the king’s gate, and was not one to pass there.
The Kedushas HaLevi says there were two different commands – first, everybody had to bow down. Second, Mordechai, as a favor to Esther, was ordered to not bow.
The Shelah HaKodesh quotes an argument in the Talmud (Megillah 12a) regarding the reason the Jews deserved death in this time period. One opinion is because they bowed to idols. The other reason is that they attended Achashverosh’s party. The Shelah continues that Mordechai’s refusal to bow to Haman served as a spiritual tikkun (or repair) for the Jews’ capitulating to bow to the idol of Nebuchadnetzer, and Esther’s eating seeds to avoid eating non-kosher food in Achashverosh’s palace (as mentioned previously) served as a tikkun for the Jews’ enjoying themselves at Achashverosh’s party. Together, their actions saved the Jews from the decree against them.