
I have had pups with acne before, in fact I think all of mine have had at some stage but it has tended to be on the belly. The fuciderm will help prevent infection (but then none of mine got infected but that may be a difference in area affected) but it won't clear it up as it is a hormone thing only time does that :)
I would have thought any kennel willing to take such a young puppy should be willing to continue with the treatment as they must be aware that such a youngster is going to require a little more care in terms of feeding etc anyway, in fact a decent kennels should be willing to do anything like this at any age and will be used to giving regular medication to dogs that require it. You could discuss it with them and I am sure they will reassure you.