I think you need to interpret "that’s a good thing" not as an approval of the civil war, but as an acknowledgement that festering conflict will inevitably reemerge in the future unless you deal with the underlying issues.
This is mirrored by how Pádraic deals with Colm's break-up with him: he isn't satisfied with the initial "just leave me alone" dismissal and probes Colm until the latter explains why he doesn't want to talk to Pádraic anymore.
And then he still tried to repair the broken relationship in all kinds of ways, including the seemingly counter-intuitive solution of standing up to Colm after hearing from Dominic that Colm expressed some admiration for that attitude after he did so drunkenly. Which of course leads to a further deterioration of the situation.
The superficial solution would be: just leave Colm alone. But this is negatively impacting Pádraic, not in the least since the island's small surface makes it hard for him to avoid his former friend. Moreover, he sees Colm having a wonderful time with other people and even "invaders" (the musician from the mainland).
Of note is that Pádraic has changed over the course of the events in the movie:
Pádraic and Colm’s feud is empathically not over in The Banshees of Inisherin ending. While he is unhinged enough to cut off his fingers for the sake of gaining some space from Pádraic, Colm shows real remorse for the first time when he learns that he accidentally caused Jenny’s death. This, along with losing his house to a fire, leads Colm to assume that he and Pádraic are now even. However, Pádraic's character has also undergone a meaningful shift, abandoning the niceness that defined him at the beginning of the film. In The Banshees of Inisherin’s ending, Pádraic decides on mutually assured destruction over peace.
While Colm hopes to secure a musical legacy for himself by getting some distance from his former friend, he ends up instead igniting a feud that seems as if it will kill both of them — in stark contrast to the idyllic setting The Banshees of Inisherin establishes in the beginning. Indeed, while Pádraic started The Banshees of Inisherin blissfully unaware of the limitations of his small-town existence, he ends the movie’s story as a spiteful, hate-fueled figure who has no interest in reconciling with Colm. Although the pair have held onto their shared humanity — as evidenced in the tragicomic moment where Colm thanks Pádraic for taking care of his dog and Pádraic assures him it was no problem — their relationship is irretrievably destroyed. With neither man making any plans to leave the island, the feud between the two is bound to just get worse and worse.
The article I linked also offers more on how the movie mirrors what happened in the civil war:
To understand The Banshees of Inisherin’s ending, the historical and cultural context of its setting is important. The film is set in 1923, at the height of the Irish civil war, on a fictional Irish island whose name translates to “the island of Ireland.” While Irish literature, poetry, and music from a few years earlier rightfully celebrated and immortalized the triumphant defeat of English colonial rule in Ireland, works that mythologized the ensuing civil war were few and far between. There was nothing beautiful, uplifting, or awe-inspiring about a war that split families and pitted friends against each other, which also helps pinpoint exactly when The Banshees of Inisherin takes place.
This is reflected in the movie:
The Banshees of Inisherin sees Colm try to cement an artistic legacy for himself by abandoning niceness, but this leads Pádraic to note that Colm hypocritically sees nothing wrong with befriending a child-abusing corrupt cop while refusing to speak to Pádraic because he is “dull.” By the end of The Banshees of Inisherin, Colm longs for a return to the dullness of his former friendship, no longer enamored with romantic ideals of suffering now that he has lost his fingers and his home to a pointless battle of wills.
However, Colm and Pádraic can’t go back, as like the country they are so close to, they are now divided by their differences, locked in a fight that will eventually cost them their lives. The character's drastic but believable evolution underscores why Pádraic is among Colin Farrell's best movie roles. In The Banshees of Inisherin’s ending, Colm gets the terrible beauty, artistic inspiration, and deep meaning he was searching for, but it comes at the cost of his friendship with Pádraic, his home, and, ironically, even the ability to play the mournful music he so loves.