"To be clear, I do expect that defending Andoran against a Chelish invasion is one of the situations in which killing others would be most justifiable. In terms of other examples...
When Andoran rebelled, this of course involved quite a lot of killing. There was a clear Good objective, the liberation of Andoran from Infernal rule, which could not have been achieved without killing people, and which achieved significantly more Good than the harm it caused; participating in Andoran's revolution was typically Good. Paladins fall if they willfully do Evil, but the Good gods chose many paladins during the revolution, and in Andoran few of them fell. I am aware of one case of a paladin of Iomedae who Fell after killing a priest of Asmodeus who had surrendered, and another instance, after the revolution, of a cleric of Milani being renounced by his goddess after engaging in vigilante murder of repentant former Asmodeans. —Clerics are held to a more lenient standard, but they do need to stay within a single step of their deity's alignment, and can be renounced for acting against their deity's goals even if they maintain their alignment.
In Galt, many more paladins fell, and many more clerics were renounced by their gods. I believe that the majority of those were during the aftermath of the revolution, but I have also heard of multiple cases in which entire farming villages were massacred in areas that had remained loyal to Cheliax, sometimes with the 'justification' that everyone there was in service to Asmodeus. Most of my information there is via secondhand accounts, which may have been exaggerated in some cases. I have never heard of anyone empowered by the Good gods knowingly participating in a massacre of an entire village and remaining empowered.
Although this is not the primary focus of the Osirion scrying project, its researchers did take the opportunity to verify whether people of various occupations were always Evil, as had sometimes been posited, along with those who had been convicted of various crimes. They did eventually find a non-Evil person who had been executed for murder, but while I don't remember the exact numbers, it took many more attempts than their efforts to find a non-Evil magistrate, soldier, or adventurer. Their reports are public, though I don't remember the specific year.
According to The Trials of the Third Crusade In Retrospect, by Ser Alard of Kenabres, one paladin attempted to eliminate demon cultists from Kenabres by executing every Mendevian with an Evil aura on sight without a trial, and Fell for it.
You mentioned the Eagle Knights; my understanding is that Eagle Knights who detect as Good typically are typically achieving significant amounts of Good, often through the liberation of slaves, and putting in some degree of effort to reduce casualties, and enforcing behavioral standards to some degree within a cohort, but I could be wrong about the details of their operations. Not all Eagle Knights, even powerful ones, detect as Good. Some self-professed Eagle Knights operate in a way nearly indistinguishable from ordinary pirates, save for their opposition to slavery, and my understanding is that those ones typically detect as Evil; Councilor Marinella Montenogor discussed a particularly atrocious case in her recent speech to the People's Council, and her staff published a transcript."
Pause. When she next speaks, her tone is a little gentler.
"Your case seems likely to have been — particularly difficult to navigate. Chelish resistance is sometimes an exception to principles that would normally be straightforward, as many extremely grave Evils that would ordinarily be handled by the law, such as empowered priests of Asmodeus attempting to damn as many people as possible, are entirely legal and in fact encouraged. Speaking speculatively, with the understanding that I may be wrong in either direction, I would expect that extrajudicial killing of empowered priests of Asmodeus necessary to prevent them from carrying out grave Evils would generally not be Evil in itself, that extrajudicial killing of other agents of the Chelish state to achieve a Good goal that could not be achieved without their deaths might or might not be Evil depending on the situation, and that extrajudicial killing of ordinary people solely for being in Cheliax's employ would be Evil. It also seems likely that a cult of Baphomet would attempt to manipulate its members into engaging in more Evil than actually necessary, with the goal of seeing them damned to the Abyss."