That's a tough one, eh? Will secular education always clash with Christian education? Yes, I think it will, unless it is made clear from the very beginning that Christ is the bedrock and Christianity is non-negotiable. Everything else will fall into its proper place if one has confidence that the place of all creation -- this physical universe -- is precisely that: the creation of God. There will be cases, despite the clear divine imprint and consistency in the universe, when the reach of the latter goes no further, because what is created cannot be greater than the Creator.
So what to do when secular knowledge, completely dislodged from Christianity, makes claims that conflict with Christianity? If you're a Christian institution, it certainly makes sense to stick to Christianity, doesn't it?