Yea I remember the prison-mission and the McCarran-missions too I think, it's been a while since I played Vegas. There isn't a "kill all the drug pushers" -mission though, although you can sort of kill many of the powder gangers along the way without getting 'mission accomplished' credit of course.
But yea, the thing is IMHO, there's just a lot of untapped philosophical etc. potential in the whole drug pusher/crucifixion/vigilante justice/torture - etc. stuff. I mean, you gotta introduce these issues to little kids at some point, why not have them in a cute game they play.
Also, Romans did use crucifixion as a part of the warfare in sieges etc., it was an 'everyday thing' for them. Pretty rough thing yea but some nations still have the death penalty. The bloody history of the Roman empire and the morality of the death penalty, more stuff for little kids to ponder about.