Auto-correcting a 0 doesn't really work for me as it will only auto-correct a 0 surrounded by spaces. But I cannot reproduce the line break either. What you can easily do is to do a search and replace with formatting, though. This won't change zeroes to highlighted immediately, but you could simply apply it a little frequently, then.
But to address your second question: For editing a grid of zeroes and ones I'd probably just use a bitmap image and use Paint, Paint.NET or whatever is appropriate. Then a simple script could convert the image into the necessary text file of zeroes and ones.