I don't think that your carputer can damage you alternator. How long have you had you alternator? I think it's probably time to change to a new one. I have been running my 1000W stero system for about 5 years and had no problem with alternator. Check to make sure your alternator is not working too hard because of bad battery.
The computer is not doing it! you sed you had a bad batt. that will make your alt charge all the time and that can kill it!
get a bosh alt with some a$$ to it and you will not have to worry oh and a GOOD batt. 900 cca at min.