In my opinion, whales and seals (and penguins etc) are not terribly important for the polar ecosystem, as they represent the highest tropic level. The loss of something like krill, on the other hand, is highly disturbing in terms of the ecosystem.
Whales are important because they are what people (the ones in charge here on Earth) like to look at, think about, and write epics about. "Save the Krill" doesn't fire up the heart and soul. We won't get people to change habits and use fewer resources in order to save krill.
And I suppose whales are *indicators* for lower tropic levels. We will only have a large number if conditions (including food sources down the chain to primary producers) are right.
Any loss in biodiversity is a crime against natture, of course - but I understand that fungal biodiversity, for example, is down considerably (here's one link, there are others:
http://nt.ars-grin.gov/sbmlweb/Research/Publications/StrategyATBI/Strategy02.cfm) .
Just a few thoughts.