Perhaps wrongly, I view the 'dark matter/energy' as simply a page marker meaning 'we don't know what it is yet'. I can't see there's a problem in this instance which requires a change to the way scientists approach their work.
Also, there seems to me a significant difference between science per se, and the way individual scientists may practice it. Scientists are simply people after all with egos, prejudices, virtues and failings.
With regard to the OP: as cofty pointed out there is no necessary connection between atheism and science. Provide an honest atheist with adequate evidence of the existence of a god and expect that person to be convinced. To react otherwise would be illogical. By adequate, I mean sufficent for the person concerned. The standard of proof required to convince each person may vary considerably.