Personally I think that besides for the objective of most accurately conveying the facts there are two considerations. A) Inculcating and maintaining a healthy respect for Jewish works, including rabbinic ones. B) Inculcating and maintaining a willingness to think and question.
The former may scare us from telling an impressionable youth that something in print as a Jewish source isn't to be taken literally. However, this risks the latter; the scenario described in the question in which an honest youth without malevolent intent is made to feel inferior for thinking.
The two considerations seem mutually exclusive to a degree. That being the case I would be tempted to just tell them the truth. Besides for avoiding the all to common case of honest youth feeling prohibited from thinking, you salvage a bit of the first concern as well, for although their respect for a particular source may diminish, their respect for the the system of rabbinic Judaism as whole will in all likelihood increase.
Furthermore, it is only by raising the stakes and putting every rabbinic word of pedestal of literal infallible truth, that such conflicts and "kofer calls" result. If one tells a child that we are meant to learn something deeper from the midrash, etc. and praises him for noting the difficulties with the straightforward interpretation (a balance between adherence to literal truth and rejection entirely) then he wont have reason to lose respect for even that individual source, let alone all of rabbinic Judaism.
The only problem with this; the last consideration, is that while one controls what he teaches his child, he doesn't control what his child will be exposed to. Thus teaching a child that its okay to consider that a seemingly fantastic midrash may have a different intent may be the best from an objective perspective, but it wont lessen the "kofer calls" that he will be exposed to.
Thus perhaps it is wise to wait until a child is capable of differentiating between his views and others views, that is maintaining a more "rational" for lack of a better term mindset while being mature enough not to squabble with others over it.
Ultimately the balance of these concerns is a "shiqul hadaas" that can only be made individually.
I have cited no sources, but as the question seemed to seek personal advice for dealing with a problem that isn't black and white, I think that presenting possible concern and a suggested course of action is appropriate.