That's right, John, science has NO conscience. Scientists do (usually).

And "was" is not the same as "should be"- the fact that people did "x" 2000 years ago has little bearing on whether "x" is the appropriate thing today. Religion also can be a useful informer, but all to often has not only no scruples, but no memory of what went wrong last time.

Examples:

Good: Sermon on the Mount, Mullah Nasruddin, Zen tales
Utterly neutral: go to church/mosque/synagogue, wear yarmulka or headscarf, food rules applied to yourself
Dodgy: social exclusivity, eye-for-an-eye, sex discrimination
Plain bad: stone the adulterers, smite the Philistines, recover Jerusalem from the Christians/Jews/Moors, enslave the nonbelievers, start an inquisition, kill the XXX people.

And they are good ------> bad independently of whether they are sanctioned by religion or not. Morality, as you correctly point out, is a matter of humans living together.