My answer was, I don't think an officer is obliged to enforce any law, which I guess makes you think I didn't answer your question. But, supposing there was such an obligation, I would say yes, the officer should resign.
"Just following orders" didn't do it for Nazi officers after WWII, and rightly so - they should have resigned, rather than following those orders. In order to prevent another Nazi Germany from ever being possible again, one has to have the option of not following orders. (The present UCMJ provides this out: a soldier has the duty to obey lawful orders.)
Let's get serious. The Nazi comparison is just a wee bit tired, unsubtle, and overdone, okay?
We agree that "lawful" is not synonymous with "just", right? So obeying a lawful order does not necessarily mean obeying a just order. (Your parenthetical conclusion seems to blur that distinction.)
My reading of the constitution leads me to think that the people of Virginia have the right, through bureaucrats appointed by elected representatives, to make a bunch of laws, rules, etc. with which I disagree. But I think the people have the right to make those laws. Sometimes I'm supporting the right of the people to make dumb laws.
Oh, here's an example. The security regs in the courthouse where I often work forbid people from sitting in the window frames, which is low and wide and makes a fine 'expedient' seat. I think that's stupid. The windows have bars on them, it would be really hard or impossible to push someone through.
This reg was made by the sheriff who in 2003 was elected to his second 4 year term by a sizable margin - which suggests the people like him.
So should I resign? I know if the sheriff learns (and he makes frequent unannounced checks, so he would learn) that I was routinely flouting his procedures I would be dismissed. And besides, he's my friend, and I'd lose a friend. But the rule is dumb. And I'm pretty sure the sheriff knows I think it's dumb.
Regarding the case in question: Woman shows up with wounds and plausible (probable) accusation. Guy gets busted. (that standard for a bust is "probably cause" not "beyond a reawsonable doubt". The guys doing the busting often don't do the investigating. The case is "investigated", which probably means statements are taken and wounds described, and the prosecutors take it to court. It is tried, and either a judge or a jury finds the guy guilty.
And it's all the fault of the police? I don't think so.