A couple of questions on that:
Firstly, if the peaceful, war-hating species you postulate were speaking with the representatives of the ship, it would be safe to assume that they have evolved to a point where they are morally-minded to judge Starfleeters based on their own actions rather than that of the ship builders or ancient history (which the crew can do nothing about). Also would such a species not forbid armed starships from entering their system/orbit, due to their beliefs?
Secondly, if that peaceful, war-hating species was in Starfleet, they've already violated their belief system by entering the Academy. As peaceful as Starfleet's intention, it is still the armed service of the Federation so all those who wear the uniform must be willing to take up arms and defend themselves, their ship(mates), or the UFP, even laying down their own lives to in the process. No officer or crewman would get out of that, otherwise they are a liability and would put others at risk.