I remember that happening one time with the Horta, where as the rest of the time it was a salt vampire that had to be killed or a crazy murderous android that had to be put down.
Hardly "the rest of the time."
"The Corbomite Maneuver": A big scary creature in a giant ship threatens to destroy the
Enterprise, but turns out to be a friendly guy who was just testing them, and they open diplomatic relations.
"Charlie X": The "monster" is a troubled child who ends up being taken care of by the only beings who can contain his power.
"Balance of Terror": The enemy commander is a decent man who regretted being ordered to fight, and destroyed himself as much to undermine his Praetor's war plans as to fulfill his duty.
"The Menagerie": The Talosians who once took Pike prisoner now take him under their protection and care.
"Shore Leave": The deadly hazards of the planet turn out to be harmless recreations.
"The Squire of Gothos": The powerful superbeing turns out to be a child, and his parents apologize for the trouble he caused.
"Arena": The "evil" alligator-people turn out to be defending their territory against perceived invaders, so the whole thing was a tragic misunderstanding.
"The Devil in the Dark": The deadly monster turns out to be a mother protecting her young, and they end up making friends.
"Catspaw": Okay, one of the aliens is evil, but the other is just a scientist trying to learn, and he sacrifices himself to try to stop her.
"Metamorphosis": The alien abductor turns out to be lonely and in love, and a happy accord is reached.
"The Gamesters of Triskelion": The brains are pretty nasty, sure, but they're defeated with a sporting wager and convinced to behave more constructively from now on, rather than destroyed.
"By Any Other Name": The invading aliens are won over by human emotions and convinced to abandon their plans in favor of peaceful settlement.
"Spectre of the Gun": The aliens who try to execute the crew are convinced we're not so bad and agree to begin diplomatic talks.
"Spock's Brain": The brain thieves are convinced to give up brain-napping and man-enslaving in favor of rebuilding a healthy society.
"Is There in Truth No Beauty?": The hideous alien is a wise and soulful being whose union with a human telepath will help the Federation.
"The Empath": The alien torturers are convinced they've lost sight of their goals and shown a more compassionate way.
"Day of the Dove": The evil entity is not destroyed, but driven away with laughter and goodwill.
"Whom Gods Destroy": The malevolent madman is cured, not killed.
"The Savage Curtain": The abducting aliens are convinced to let our heroes go because of good sportsmanship. Or something.
Okay, there are a significant number of "destroy the evil thingie" stories in season 2, and to a lesser extent in season 3, but they're more than balanced by stories where the threat turns out to be not evil after all, or where it's defeated/escaped through ingenuity and noble principles rather than brute force.
And then of course in the animated series, they almost always resolved the crisis without violence, except in "The Slaver Weapon."