Knockout.js seems to be clobbering my jQuery event handlers, how rude

Rather than overriding the base checked handler, just create your own custom binding to update the UI.

Here’s an example of a model and a custom binding to handle updating the UI:

var Model = function () {
    this.checked = ko.observable(false);
};

ko.bindingHandlers.customCheckbox = {
    init: function (element) {
        // Create the custom checkbox here
        $(element).customInput();
    },
    update: function (element) {
        // Update the checkbox UI after the value in the model changes
        $(element).trigger('updateState');
    }
};

I’ll bind the model to the following HTML:

<input type="checkbox" name="genre" id="check-1" value="action" data-bind="checked: checked, customCheckbox: checked" />

And really that’s all I’ll need to do.

Here’s an example: http://jsfiddle.net/badsyntax/4Cy3y/

[edit] – i think i rushed through reading your question and didn’t get the crux of what you were asking. I’ll leave my answer here in any case.