How to disable system apps, or controll which apps launch automatically? I've been having this problem where the Navigation app launches every 10 or so seconds.

I've heard this is because some pins are short-circuited.

I've tried to install 2 apps that should make this problem go away, but so far nothing worked.

I'm left with trying to control the lifecycle of these apps. They are system apps however, and I can't uninstall them.

Is there any possibility for me to hack my Android a little bit and disable the threads that control these apps?

I'm talking about a HTC Desire HD, 2.3.5. Android version
Aside from rooting (temporarily or permanently), you can't disable the system apps prior to Android 4. Your particular case may have a ray of hope, though.

Alternate app responding to Intent

If the navigation app is responding to an Intent, you could try to find a different app that responds to the same Intent. You'd get a pop-up to choose which app to open when the pins short and the Phone thinks it has been docked. 

Alternate app that can do nothing

Ideally, you could find an app that responded to that Intent and did nothing as a result. Then set that as the default handler.

Task killer

Another possible option is to use a task killer (a rare good usage of such an app). There should be some that have the option of killing an app as soon as it starts; if not, the free app Llama can do that, as can other automation apps like Tasker.

Rooting

If none of the above work, you may want to root your phone. This will let you uninstall (or simply freeze) the navigation app so that it doesn't open up.

Fix/replace hardware

The last resort, and probably most useful, is, of course, fixing/replacing the hardware.