To put it bluntly, yes
The meaning of "thins them out" is just what it looks like, it's simply funnier to just mention it in passing like that and not dwell on it too long. The narrator doesn't take it too seriously and the reader isn't expected to take it any more seriously than Peter does, but it definitely happens. Denial of this aspect of the Lost Boys seems more rooted in a cope about what Peter should be than in how he's actually, unapologetically characterized as in the book.
Peter's emotions, loyalties, and even enmities are keenly felt but fleeting and fickle. By the end of the story, he's forgotten Tinker Bell and Captain Hook ever existed at all.
Peter routinely strikes fairies, creatures no taller than a young child's still growing hand.
Fairies indeed are strange, and Peter, who understood them best, often cuffed them.
The Darlings have reason to think that Peter might stop rescuing them from certain doom if it ever starts to get too repetitive and boring for him.
Certainly they did not pretend to be sleepy, they were sleepy; and that was a danger, for the moment they popped off, down they fell. The awful thing was that Peter thought this funny.
“There he goes again!” he would cry gleefully, as Michael suddenly dropped like a stone.
“Save him, save him!” cried Wendy, looking with horror at the cruel sea far below. Eventually Peter would dive through the air, and catch Michael just before he could strike the sea, and it was lovely the way he did it; but he always waited till the last moment, and you felt it was his cleverness that interested him and not the saving of human life. Also he was fond of variety, and the sport that engrossed him one moment would suddenly cease to engage him, so there was always the possibility that the next time you fell he would let you go.
Peter lets the Lost Boys starve eating imaginary dinner that only Peter is sated by, and he has a 19th century schoolteacher's method of keeping them in line playing his game.
The difference between him and the other boys at such a time was that they knew it was make-believe, while to him make-believe and true were exactly the same thing. This sometimes troubled them, as when they had to make-believe that they had had their dinners.
If they broke down in their make-believe he rapped them on the knuckles.
To have an adventure, Peter proposes waking up a pirate just so they can kill him.
“What kind of adventure?” he asked cautiously.
“There’s a pirate asleep in the pampas just beneath us,” Peter told him. “If you like, we’ll go down and kill him.”
“I don’t see him,” John said after a long pause.
“I do.”
“Suppose,” John said, a little huskily, “he were to wake up.”’
Peter spoke indignantly. “You don’t think I would kill him while he was sleeping! I would wake him first, and then kill him. That’s the way I always do.”
“I say! Do you kill many?”
“Tons.”
John said “how ripping,” but decided to have tea first.
But most relevantly,
Peter nearly kills a Lost Boy in Chapter VI
“She is dead,” he said uncomfortably. “Perhaps she is frightened at being dead.”
He thought of hopping off in a comic sort of way till he was out of sight of her, and then never going near the spot any more. They would all have been glad to follow if he had done this.
But there was the arrow. He took it from her heart and faced his band.
“Whose arrow?” he demanded sternly.
“Mine, Peter,” said Tootles on his knees.
“Oh, dastard hand,” Peter said, and he raised the arrow to use it as a dagger.
Tootles did not flinch. He bared his breast. “Strike, Peter,” he said firmly, “strike true.”
Twice did Peter raise the arrow, and twice did his hand fall. “I cannot strike,“ he said with awe, “there is something stays my hand.”
All looked at him in wonder, save Nibs, who fortunately looked at Wendy.
First, Peter is shown as not really fully grasping any difference between make-believe-dead and real-dead, and wishing to pretend it never happened rather than deal with reality.
Second, the Lost Boys all fear Peter's wrath and fully expected him to want to kill whoever did this, none of them dare to raise any objection or openly oppose him when he prepares to strike Tootles.
Third, this is probably a rare and surprising situation, odds are that most people Peter tries to kill aren't also begging him for death, which might be why Peter finds himself surprised and struggling for a few moments to follow through. Righteous vengeance is much less satisfying when the target is contrite and seeking atonement.
Fourth, the narrator specifically points out that "fortunately," one Lost Boy looked at Wendy. It's fortunate that happened, implying that in the counter-factual where nobody swiftly informs Peter that he doesn't have to avenge Wendy because she's not actually dead, something very unfortunate would have happened.
Finally, this incident of Peter showing a restraint on his righteous anger is very surprising to the other Lost Boys, which implies this is definitely unusual for how Peter handles people who anger him. Everyone who knows Peter best fully expect him to be as merciless to a Lost Boy who's earned Peter's ire as he is to a pirate.
And growing up into a man definitely earns his ire; like it says right there in the passage, it's against the rules! Why would you go and break the rules like that? The concept that growing up is an involuntary process is beyond him, he's Peter.
But this is all badly overthinking this
Dissecting humor is like dissecting a live frog: at the end of the process, you've killed it.
The narrator said it happens, therefore it happens. You're really just supposed to laugh a little and quickly keep on reading. Dwelling on it and whether or not Peter would do that is like fretting about how irresponsible it is to leave babies in the supervision of a dog. You're not really supposed to start trying to apply grown-up logic and morality to Peter Pan of all characters.