What is the lingering feeling at the end?
I think the lingering feeling is one of confusion, and an incredible loss of innocence. As the officer approaches and suggests that they ought to "have been able to put up a better show than that," perhaps the idea that they wouldn't be running around like savages, he brings with him a very unsettling idea that he is representing the same evil, the same tendency towards violence and destruction, even with the nice trappings of the uniform and supposed discipline.
The officer is uncomfortable with the childlish display of crying and broken down boys and turns to look at the "trim cruiser in the distance," the means by which he practices destruction and brings death with all its incredible power.
To me this suggests that the boys are really no better returning to "civilization" and that their loss of togetherness and innocence is common to all, not just the boys on the island.
The lingering feeling which Ralph has at the end of Lord of the Flies refers to the initial enthusiasm the boys had at the beginning of the novel. The deserted island could have become a place of utopian peace and tranquility for the boys, controlling their own lives without the supervision of adults.
"It was like that at first," said Ralph, "before things--"
"We were together then--"
... For a moment he had a fleeting picture of the strange glamour that had once invested the beaches.
Ralph envisioned what could have been before the uncivilized savagery began.