I have been working on a similar "empty base" idea to allow hidden movement within the rules of the game. Specifically with regard to Elf Cloaks ("house" rule to be posted this weekend once I work out some final details). I think your use of it in this case is great.
A few suggestions (since you asked):
To best represent what is depicted in the movie and in the book, you will want to leave out the Wargs for sure. Besides being inappropriate in this scene, they also really tip the balance with regard to catching the hobbits due to thier extensive movement.
Likewise, do not give Aragorn Anduril. He's a capable enough warrior for this scenario without it and he did not get the sword reforged until the third movie.
If any captured Hobbit has suffered a Wound, the Evil player cannot score a Major Victory regardless of other conditions ( "Alive and Unspoiled", remember?
)
Don't deploy the Hobbits seperately. It immediately tells the Evil player who is who. Instead, perhaps try this:
4x4 board. One edge of the board is labled as the river and the opposite end will be called the "Amon Hen" edge for lack of a better term. Amon Hen is placed on the center line of the table 12" from the Amon Hen edge ( the side opposite the river). The remaining two sides of the table will be called the "forest edges" here.
The good player must deploy all four Hobbits, Borimir and Aragorn within 6" of Amon Hen. Borimir and Aragorn must be at least 12" from each other. Gimil and Legolas start within 6" of the river.
The evil player divides his forces in half and will deploy one half on each of the two "forest edges", within 6" of the edge.
Frodo must escape by moving off the River edge of the board.
I obviously haven't play tested this so some of the deployment measurements may need to be tweaked for balance.