The D&D 4e combat system was set up to be small skirmishes with no more than 20 or 30 on a side, which it does fantastically well, all fairly fast conflicts. To accomplish what you want to do you will have to make the combat feel grander, without over loading yourself. First things first you as the DM should have the 2 outcomes already written down, with how they are reached. (EX: Party wins if they can fortify the city effectively and develops a weapon or device that can assist in the defense of Winterhaven, the party losses if any of the conditions for victory are not met.) Keep It Simple.
The next thing is prep, on your part it will be a lot of storytelling, scene painting, and plot build up to make the event as moments as a battle should be. The players should have a war council before the battle where they give the NPC’s there orders, figure out how they are going to go achieve their goal. (EX: The party will help the people of Winterhaven to fortify the wall around the city, show them how to use spears and will use Old Man Jenkins Vodka to make explosives. The road into town will be blocked off and trapped with fall pits.)
When the fighting comes you will, have the characters barking orders, run to and fro to shore up the holes in the lines and trying to deal with the chaos of all out war, have one or two encounters prepared based on what the party came up with (EX: leader of village “Hay they have a dragon that we were not expecting so you need to kill it”). No matter what remember that what the characters do should impact how the battle goes, the story is about them not the hundreds or thousands that will fall to the swords of the enemy in their name. Building should burn the land should be scorched, the area should be marked by the battle, but the vast numbers that are fighting never have to roll for damage, the battle should follow the logical paths of chaos.
The battle is over and won, now come the questions. Who died? Who lived? What was burned? What did we save? Did the BBG get away or was he even here? Each answer is different for each battle and how you would like the story to build from there. (EX: GM “Your preparations saved the town of Winterhaven for the goblin hordes, in total 30 villagers are dead, 56 are wounded including the eldest son of the barkeep Brindle who helped you in slaying the dragon. The goblins lost over 300 of their warriors and retreated shortly after the dragons death. The church was burned to the ground by dragon fire and Old Man Jenkins was vary displeased to find out what you used his good stuff for.) Give out exp to the party for completing 2 major Quest plus the exp from the encounters and skill challenges they were in.