There is neither violence nor sexuality in the story. However, by the
end it seems clear that being born as a haibane is entering some sort
of afterlife--evidently only available to children--and that Reki is
working out some sort of salvation after having committed suicide. At
least that is how I read it, but whether that was the writers intent or
not, the suggestion of suicide and despairing of salvation are very
much present in the last episode.
Parents who are unwilling to discuss the issue of suicide, or for that
matter their own faith's teachings concerning the afterlife and
salvation, with their children should be warned against what otherwise
is a very lovely story.
In any event, because of the issues involved in the ending, I think
Haibane Renmei is unsuitable for children under Rakka's apparent age of
12. (And for other reasons it will bore most boys silly.)