In order to assimilate into a society there is a cultural minimum one must adhere to and if participating in public ceremonies - causing no harm to anybody - is part of that then it should be expected that people will go along with it in exchange for belonging to that society (this can also be applied to people within their native culture).
However, on the other hand it is very likely that those boys did not choose to leave their birth country and go to Switzerland. In these circumstances they cannot be expected to have the social or emotional maturity to be pragmatic enough to deal with a situation requiring them to go against their early social education (especially considering the recent trauma related to their upheaval). It is also true that it is not fair for someone of any age to be forced to leave their home culture and - clearly - fitting in with another that goes against ones's ways of life must be very challenging.
I therefore do not think that these expectations for levels of assimilation should be applied to minors. Furthermore, it seems reasonable to give adults an adaptation period of, say, five to ten years after which they can be considered for permanent citizenship. In the meantime, why not accord them all the rights of citizenship if they meet the asylum criteria.
Understandably, it was possibly an embarrassing incident for the officials involved however this unease could have easily been turned into an opportunity to educate the children present about diversity, pluralism, and tolerance.