I haven't checked properly, but you can probably implement that logic here. If you simply remove the output inventory from that line, it should just destroy those items when changing recipes. If you don't want to lose them, you can add a check into that function that just returns false if there's anything in the output inventory. That should halt the combinator until the items get cleared out by other means. It will probably also make the "Not enough space in chest" error pop up, but that's just cosmetic and can be solved by returning something other than a boolean and then checking if the message should be shown or not based on that.
I would probably just add the option, but I've been pretty busy lately and already have a bunch of other stuff in the backlog for this mod, so don't hold your breath...