As of the latest, latest snapshot (14w02b), this is most certainly possible. In fact, there's an easier way to do the whole thing now, which is awesome. With the /blockdata command added in the snapshot, you can modify and overwrite the contents of a tile entity (including a chest), and much, much more. The applications of /blockdata go beyond what I can fully comprehend at this point in time, but, for this specific case, it's not too hard.
Let's say for example your equipment chest is supposed to contain a notch apple, a gold sword, a bow, and a stack of arrows. The command for that would be /blockdata X Y Z {Items:[{id:322,Damage:1,Count:1,Slot:0},{id:283,Count:1,Slot:1},{id:261,Count:1,Slot:2},{id:262,Count:64,Slot:3}]}, replacing X Y and Z as appropriate. There's a lot of stuff going on in that command, but essentially, you are changing the data of the chest to contain the specified items. It's the same concept as using /setblock to spawn a new chest with these items, except instead of replacing the chest, you're overwriting its data.
In this more specific case, you want /blockdata 264 4 997 {Items:[{id:274,Count:1,Slot:0},{id:275,Count:1,Slot:1}]}.
And, of course, if you want an empty chest, all you need to do is use /blockdata X Y Z {Items:[]}
Best Answer
You must use a comparator on the hopper (with one powered rail above it), than a redstone torch to activate it.
Check bellow:
What happens is that when the minecart move one item into the hopper, the comparator detect this and send one energy pulse to the repeater, that energizes a block. This guy have a redstone above it that charges a second block with a redstone torch on it, consequently deactivating the torch and unpowering the rail. When all items were moved to the chest, there's no more energy, so the redstone torch power on and activate the rail, forcing the minecart to move back.
IF YOUR MINECART CAN'T GO BACK:
The same system above, the difference is that you need a detector rail 1 block far from the hopper and the powered rail must be going down: