Not to belabor the point, I like to think we name ships for battles to honor the cause and the men who fought them rather than the fact that there was a war or to glorify battle.
Maybe that would be sufficient for the aliens?
Do we only honor certain battles, though? I mean, history is written by the victors. We generally don't name ships after defeats.
Some of the battles are named after their location. Yorktown could just as easily be defined as being named after a location on Earth. Or a historic location on Earth.
The US lost a battle to the British at Charleston during the Revolutionary War. If there is a USS Charleston, is it named after that defeat or is it named after the city? After all, there are many historic connections to Charleston besides the Revolutionary defeat.
And who says its a defeat? We're talking 500 or 600 years after the Battle of Yorktown or Battle of Charleston. The Earth is united. Whose history do we honor when commemorating victories? An American victory is a British defeat and vice versa.
If we're honoring the lives of those sacrificed, then would it be acceptable or repugnant to have a USS Dachau, USS Auschwitz, etc...?
We had a topic a while ago where the OP was berating the idea of naming a ship the USS Cortez (or was is USS Coronado?). History paints these explorers as just that, explorers. However, history also reveals these people were murderers, rapists and conquerors bent on pillaging and subduing indigenous peoples.
One person's hero is another person's savage. "Why is your ship named the USS Crazy Horse?"