Several ways to look at this decision:
1. As an extremely dangerous precedent, by declaring a species "threatened" based on the results of modeling nearly a hundred years into the future.  The error bands on such modeling are usually quite wide.  Yes, warming is occurring now and likely into the immediate future.  But humanity and other parts of nature may change the trend in ways we may not foresee now (clouds, winds, etc.).  Since Congress did not define ESA terms such as "foreseeable future", the agencies (NMFS, FWS) use their own discretion on defining the term for each project, hopefully based on reason and not speculation.  The court thought that was all ok in this case.
2.  Will the determination make a difference?  Bearded seals, as all marine mammals, are already protected by the MMPA, which requires mitigation usually not that different from that required by an ESA consultation.  Feds consult under the ESA (takes longer), while companies provide the info under the MMPA.