Can I use Karabiner to disable built in keyboard during start up
No, Karabiner won't help here, because it first has to be started to disable the internal keyboard.

You have not elaborated on why the key is stuck, but maybe you can fix it? 
https://www.ifixit.com/Guide/How+To+Fix+Sticky+Keyboard+Keys+on+a+MacBook/37709 shows you how to remove a key cover from the keyboard. There are also videos out there. 
Also Apple has a guide you might want to check: https://support.apple.com/en-us/HT205662