Can we prevent or detect Console popup event?

You could use this onCustomConsoleComponentButtonClicked() to track the click event and setCustomConsoleComponentWindowVisible(false) to close the window.

Along with that, make window height and width to 1 pixel. (Though we cant make it 0).

<apex:page showHeader="false" standardStylesheets="false">
    <apex:includeScript value="/support/console/34.0/integration.js" />
    <script type="text/javascript">
            var eventHandler = function (result) {                 
            closeWindow(result);
        };

        var closeWindow = function closeWindow(result) {
            sforce.console.setCustomConsoleComponentVisible(false, result);
        };

        sforce.console.onCustomConsoleComponentButtonClicked(eventHandler);
    </script>
    <h1>
        This Space Intentionally Left Blank
    </h1>
</apex:page>

For more information, Refer onCustomConsoleComponentButtonClicked() and setCustomConsoleComponentVisible()

I have tried that, window is closing on clicking footer component.

I would think you should be able to listen to that event using a click listener. The toolkit has an addEventListener method, so something like:

sforce.console.addEventListener('click', function (event) {
    // check if the proper component was clicked
});

You can also specify tabId in an optional third parameter (additionalParams), if you want to limit the scope of this listener.

I can't reproduce your layout to determine any further steps, but it ought to fire.