If we're going to discuss these utterly ridiculous rules in the first place, we have to stick by the exact letter of the rule, and the rule says evil outsiders cause lingering evil only on the Material plane. By the way, it says 'evil outsiders'. It doesn't say things with the [Evil] subtype. Any outsider with an evil alignment, regardless of its subtype, plane of origin, or whether it acts on its evil alignment, apparently causes lingering evil, according to that rule. And it makes no exceptions for outsiders of the native subtype. If we're using that rule as an excuse for murder, then it means that murdering every single outsider of any subtype that pings on detect evil and is on the prime material plane for a 'long-term', whatever that is, is justified, including tieflings, genasi, etc.
The rest of the stuff mentioned here has no rules by which to judge it on, and therefore can't come into a nitpicky discussion based solely on a stupid set of rules. There are no actual rules for sections of one plane sliding into another - it happens, but there are no rules on it, therefore there's no way to actually account for it in such a nitpicky discussion. It exists purely in the realm of DM fiat.
This is only given with the justification of 'because it still stops the creature's predations on the innocent.' If the creature has made no such predations, there is nothing to stop, therefore it wasn't justified and it is murder. Just because you think someone is likely to cause harm doesn't make it true, and if it's not true, then the murder is not justified and therefore evil. So, you could be trying to stop someone from harming others, but you're acting on wrong information. Still murder, just as if I overhear you plotting to kill someone, murder you to prevent it, and it turns out you were talking about doing something in a game, I still committed murder.