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.
That reply rates "John Kerry" on the "clarity/nuance" scale.