Car battery when bad when starting, alarm now goes off when opening door to start car but car won't start now. I think thwe battery is fine but the car now won't let me start it. Is there a way to disengage the system so the car will start?

You gotta tell me much more like the car, the age of the battery and the alarm in question. Most aftermarket alarms require you to hit the disarm button 2x when it is going off. WHen you press it once, it turns the siren off, when you hit it again, it shuts of the alarm.

Also, some alarms have a setup if you unplug them, the starter will still be disengaged so not sure if that will help. You really need to get a voltmeter and hook it to your car when you crank it over to see what the voltage is. Sometimes you have have a bad cell in the battery. That makes everything look fine until you put a heavy load on it. If you have wild voltage drops, it puts a major strain on the car's whole electrical system and can trigger the alarm to sound off even if it was disarmed in the beginning.