Car Alarms: car alarm problem, mustang cobra, override switch

Question
My mother has a 1995 mustang cobra with after market alarm system called Rebel security system. Yesterday the cars battery was disconnected, after reconnecting the car would not crank.                                                The red light for the alarm was flashing, the main alarm box under the dash was clicking.There is another box inside the console that has been disconnected. I looked for a valet override switch could not find it so I disconnected the main wiring harness that powers the starter horns and locks etc.So both boxes are disconnected.
Now the car cranks there is no clicking or red light flashing.This alarm system has caused her many problems before.
Is it safe to leave the wiring harness disconnected and drive the car without any problems happening to the car ?
Does the system need to be uninstalled completely?  

Answer
Ok, remove what is NOT from Ford, repair the wiring.
Especially the relay that was installed inline
on the starter wire (off the ignition switch harness)

Then start over with a fresh set of remotes and an alarm
mom can undertand and operate.
Makes for a better experience.

Get the wiring for it at www.wiringcharts.com , identify
the wiring, remove, repair and restore.

Good luck.

ALARMTEK