There are two basic ways of treating time travel in fiction:
1. There is one timeline. If you travel back in time to cause an event, then that event is predestined. You will do it because you've already done it. Any story that has characters change the timeline is contradictory.
2. There are alternate timelines. Any time you change the timeline, you're actually crossing into an alternate one. In this case, the crew can either travel back in time or not. If they choose to, then its a predestined event in their own timeline. If they choose not to, then they are crossing into another timeline where there never was a colony. As you say, this is only possible when characters from the colony timeline interact with characters from the non-colony timeline. This is not contradictory.
This is sci fi, so the writers could be using either scenario. If you & Pavonis are correct, then they're using scenario 2 and there's no paradox. The reason I don't believe they are is that the major ethical issue was whether to go home and erase the colony from existence. If there are alternate timelines, then they could just go home and the colony would still exist in another timeline. We know this is true because the colonists in the first timeline must exist to erase the colony in the second.
The structure is either a loop back to itself or a cross to another timeline. They chose the second option. But if they've crossed, then they left rather than erased the colony. The colonists still exist in the first timeline, and never existed in the second timeline. So they did no harm by leaving.
The ethical issue only arises if they're actually erasing those people. And they're only erasing them with the single-timeline premise. But this is contradictory. Maybe you guys are right and I'm misunderstand the writer's intentions. If that's the case and there are alternate timelines, then what's the ethical dilemma with leaving?