If you expect this to be a something fairly "permanent", with maybe only the occasional change done (software upgrade, etc), you might want to look into purchasing pre-bootloaded ATMega8/168/328 chip(s), 28-pin DIP socket(s), the necessary capacitors and resonators, and build the circuit on a protoboard (or etch and drill your own custom PCB). Solder a socket to the board, then install the microcontroller into the socket; when you need to change it, remove it from the socket, mount it in an Arduino in place of the Arduino's regular CPU, program it, then swap it back.
Another option would be to build a ZIF programmer onto a protoboard shield for pre-bootloaded ATMegas (basically, all the pins for programming the Arduino, with the exception of the clock/resonator pins, are brought up via the shield pins, so - in theory - if you remove the CPU from the Arduino, then mount a ZIF socket to a protoboard shield, wire the pins up properly to the headers, then add the resonator circuit, and put the CPU in the ZIF socket and then mount the protoboard shield to the "brainless" Arduino - you should be able to program the Arduino in the ZIF socket just like it was in the normal socket).
You could also integrate an RBBB (Really Bare Bones Board) into your interface, instead of using an entire Arduino (kinda a step between an Arduino and a custom ATMega8/168/328 CPU setup).
Even better, add header pins connected to the proper pins (TX/RX, etc) and buy an FTDI cable, and you can make the device "field programmable".
With all of that said, I am not necessarily sure you even need to worry about the wires working loose; there was a guy on these forums who hooked his Arduino up to his combine harvester (!) as his first Arduino project (!!) to use the Arduino to steer the combine (via a hydraulic servo control) on straight paths in his fields (!!!) using GPS. He mounted his Arduino on a board, which was inside a snap-lid plastic container bolted to the front/side of the tractor. The wires were just fitted in the sockets; I don't even think he dropped some hot glue on them. He said he never had a problem with them vibrating loose on the tractor for the entire harvesting season.
Maybe you should worry, maybe you shouldn't. Hot gluing the wires on the board may help. Otherwise, think about another option like the RBBB or a custom socketed CPU...