There is no circularity.
Lets say that I calculate mutation rates based on the genetic difference in modern people compared with a biblical date of 4004 bc, and come up with a figure. If I later take the above calculation and use it to disprove humans/apes sharing a common ancestor 4.5 million years ago with you accept this as objective evidence or as evidence from circularity?
The mitochondrial calculations are not set out to prove evolution.
My calculations above were not directly set out to prove creation either. However since they are based on it they are not in themselves objective evidence against a macro-evolutionary scenario witch does not have humans being created 6,000 years ago. In the same way though the evolutuionary mitochondrial calculations are not directly set out to prove evolution, the fact is they are based on it (humans and chimps sharing a common ancestor) and are not objective evidence against a recent biblical eve (as they commonly presented as being).