So, then... And please answer this seriously as I mean it seriously. Is the science of embryology and human development "atheistic"?
I've never seen a science text of any description anywhere that teaches embryology as anything but a purely naturalistic process. Yet the Bible asserts repeatedly (sometimes directly quoting God) that God is personally and intimately involved in the creation of individual humans beings; and not just "souls" but the physical body as well. See the standardly cited anti-abortion proof texts: God "forms inward parts" in the womb, he "knits" fetuses together of bone and sinew, etc.
If embryology is not atheistic, then how is it not atheistic while evolution is? Or if embryology is atheistic, then why has no one ever (to my knowledge) complained about it's teaching.
I'm genuinely curious about this.
Not necessarily. Please understand that to undertake science either theistic-ally or atheistically does not require the intrusion of presuppositions at every point. If you ask me, this whole controversy is way overblown. Good science can take place with various presuppositions.
The case you mention here may see benefits without regard to either presupposition, namely creationism or evolutionism. The reason few people complain about the science of embryology is that it treats of a highly specified process within a limited range of observation.