Some may claim that Cryptic is forcing the lore to work for them, but even during Deep Space Nine the Klingons withdrew from the Khitomer Accords and attacked the Cardassians. Now, much of that was due to internal sabotage by the Dominion, but the Klingons readily embraced war anew as there was a general sense that as a people they were growing weak. It's most decidedly not a stretch of the imagination that such feelings wouldn't fade away with time. Klingon dissidence boiling to the surface 30 years later and resulting in all out war between them and everybody else seems pretty believable.
Beyond all the lore reasons, there's a valid excuse for a combat focused Star Trek MMO. Anything else would appeal to such a finite group of people that it wouldn't be financially feasible unless you developed the title as a flash-based game. Also, it's a lot more fun this way.
Fighting is enjoyable because conflict is within our nature. In Star Trek, it's laser gun shoot-outs and giant space ships framed in dazzling lights and explosions. Yes, there are more ways than one to experience this universe, but the perspective of a captain during a time of war between the Federation and Klingons is a perfectly valid -- if not the most interesting -- choice.
Exploration, diplomacy and philosophy are all aspects of Star Trek. Conflict is the threading that ties them all together. When exploration into a new solar system results in the discovery of a hostile entity, we get conflict. Conflict leads to negotiating, and if that breaks down it results in all out combat. Even philosophies, many of which differ between species, often leads to various kinds of conflict. In this scenario, combat is the elephant and all of these people claiming it's something else are blind men holding onto different parts of the same creature.
And really, can't we get past this and focus on what's important? Whether or not the game is any good.