I personally think that it's still a concession to the perceived mores of our society, and the juxtaposition of violence and sex. While the show pushed back a bit against the idea that seeing nudity in a sexual context is abnormal or wrong, or at least that it was silly to try to hide nudity when they weren't censoring violence, there was still a perceived moral line in portraying anything violent, like a crucifixion/execution with nudity. This seems to me to suggest that the show did not move very far from the notion that nudity is sexual, and executions/crucifixions are not sexual and therefore crucifixions are not done naked. Even if the creators of "Spartacus" did not themselves equate nudity and sex, it appears to be an acknowledgement that many viewers would equate the two, even in the context of a crucifixion, and seems to suggest at the very least, that someone had an idea that even a hint that there might be an erotic aspect to a crucifixion was wrong, or would be disallowed by network censors on that basis.