The incident intensified Joseph's anger toward the Founders and cemented his belief that everyone should have the right to a fair life. He resolved to prevent others from dying while working with Arkoral. Stephen's death may have contributed to Joseph's desire to start the Resistance.
Stephen's death may also be the reason why Joseph uses the moniker "brothers" to refer to the members of the Resistance (as opposed to other monikers, such as "comrade" "rebels" etc.). It could be to both instill a sense of unity in the Resistance, and to honor Stephen's memory.
In the introductory scene for the Resistance campaign, Joseph is seen using the sun's rays magnified through a pair of broken glasses to light his cigar. Given that Joseph does not wear glasses (and even if he did, a pair of broken glasses would be worthless to him), it's implied that they're a memento of Stephen, who may have worn them.