position : fixed; will avoid the automatic scroll to input as it won't be in the scrollable area.  
Here is a fast written example, based on this answer, and using jQuery, sorry…
CSS 
.hiddenInput{position: fixed; opacity: 0;}
jQuery 
    var inputTop, inputBottom;
    window.onload = function()
    {
        inputTop = $('#input').offset().top
        inputBottom = inputTop + $('#input').height();
    }
    function isScrolledIntoView(el)
    {
        var docViewTop = $(window).scrollTop();
        var docViewBottom = docViewTop + $(window).height();
        return ((inputBottom <= docViewBottom) && (inputTop >= docViewTop));
    }
    function hideInput()
    {
        var el = $('#input');
        if ( isScrolledIntoView(el) ){
            el.removeClass();
            }else{
            el.addClass('hiddenInput');
            el.css({top: inputTop});
        }
    }
    window.onscroll = hideInput;
working fiddle