HO-LEE THREADJACK BATMAN!!!
To state the obvious, a major university's academic program is generally going to be recognized as better, or at least more prestigeous, than a Christian school. I'm speaking here of the PCCs, Bob Jones, Liberty, et al., not Notre Dame, SMU, Duke, and other "real" colleges that are supported by religious denominations. Yes, the ancient Aramaic may be to die for, but a degree in Youth Ministry from PCC is not going to open the same doors that even an English degree from Cal Berkeley is.
Go to a Christian college if you want to live in that environment. Personally, even as a practicing church-goer, I'd rather rub salt into my urethra than go to college under the PCC rules. If you want to grow spiritually and in understanding of religion, they're the right place.
If you want a more conventional education taught by recognized scholars in their fields, go to a normal major institution.
Also, recognize that none of the small Christian schools have ROTC programs and that some have accreditation issues that will keep grads from even OCS or PLC-type programs.
My advice would be to attend a normal school with a strong program in the major you're interested in, and just hold true to your own religious beliefs while you're there.