ALPA, for all of its faults, cannot run the airline. The way that Colgan integrated the Q400 into its fleet, trained (or more properly didn't train)the pilots, hired pilots, and managed (or more properly, mismanaged) the Q400 in day to day operations, helped to cause this accident. Period.
ALPA cannot mandate training, manuals, and qualifications. These are the job of the management team, with oversight from the FAA.
While in a perfect world, ALPA would raise these issues with airline, or if that fails, raises them with the media, they are treading on some thin ice if management decides to push back, which a management team with Colgan's reputation most certainly would.
Accident investigations are about assigning blame to the most judgement-proof involved party, at this point. Regarding safety, its rapidily approaching every man for himself.