This is not a bug related quest conflict, I get annoyed with people thinking it is. Hardin survived the NCR attack on Helios One and hates the NCR with a passion, this all comes out in his dialogue, why would anyone expect to be able to get him to say oh okay I was wrong and ally with the NCR? Sometimes you make a decision that will preclude you from making alliances or ending the game in a certain way, that's a good thing.
You are making an assumption of what a character would think or would not think, which isn't exactly the same as game mechanics...
Strictly going by the definition of a coding bug, it is not a coding bug; however, it is an error/oversight in quest development. If you help Hardin become overseer first, and then you follow the NCR quest, the NCR quest still gives you a choice (destroy/diplomacy), but in reality, you cannot make a choice, because there's no dialog trigger/option to even ask. So, a ) there should be a quest check to see who the Elder is, and based on that, either give you the destroy/diplomacy option, or just the order to destroy; or b ), a dialog trigger where Hardin tells you he will never help the NCR.