Is a bacon double cheeseburger a greater violation of the laws of Kashrut than a cheeseburger, or do they count equally, and why? Does it matter if the cheese and meat are both Kosher?

The Torah prohibition of milk and meat applies only if both are kosher. In that case there is a Torah prohibition of cooking the two together, and of deriving any benefit from the mixture, whereas if either the meat or the cheeze are from non kosher sources (i.e. from a non kosher animal) then those prohibitions do not apply and the only thing forbidden is the eating. In either case eating is a violation of a Torah commandment.