Was Tsukiko a godless cleric?

[hroþila]

Then why would they keep giving her spells after she helped destroy their capital?

It wasn't their capital, it was one of the main Southern cities.

Anyway, the Twelve work as a pantheon, and there's little indication that they would all agree to do something like that, not because they're happy that Azure City was taken but because of the implications. Evil gods wouldn't necessarily like the precedent this would create because it could likely be used against anyone plotting an Evil scheme in the future, as those could have bad consequences for other cities or nations too. Especially because stripping Tsukiko of her divine magic wouldn't actually have changed anything (they presumably couldn't take away the Inflict Critical Wounds that Tsukiko used during the battle to heal Xykon even if they had wanted to because that one had already been granted, and she didn't do anything critical after that).

Alternatively, the Twelve might have agreed that Tsukiko had a real shot at exposing Redcloak's true plan to Xykon, which would have been the immediate end of the Snarl threat, at least for the time being. And in order to do that she needed to keep her place in the Gobbotopian hierarchy, for which she needed her spells.