Yes this is possible, basically, when the device boots it will be being forced to boot up your Navigation system using a registry key. You need to locate this key and remove it.
It will be similar to
[HKEY_LOCAL_MACHINE\init]
"Launch10"="shell.exe"
"Launch20"="device.exe"
"Depend20"=hex:0a,00
"Launch30"="gwes.exe"
"Depend30"=hex:14,00
So Launch30 will probably be your application, so just delete that one. A standard mobile registry editor should let you do this, but getting it connected to the PC is usually the issue. Most devices have weird soft buttons that can be held during a re-boot to pause boot and allow you to connect.
These is also another small application that you can get to show/hide the windows task bar on these devices to allow you to run your applications full screen (As Tom Tom won't and your taskbar will always be onscreen so when you tap the bottom you get windows interfearance)