Make overlaying div on leaflet not click through

You could move your overlay div outside your map and then position it above it using negative margins and z-index. Here you go:

// We’ll add a tile layer to add to our map, in this case it’s a OSM tile layer.
// Creating a tile layer usually involves setting the URL template for the tile images
var osmUrl = 'http://{s}.tile.osm.org/{z}/{x}/{y}.png',
  osmAttrib = '&copy; <a href="http://openstreetmap.org/copyright">OpenStreetMap</a> contributors',
  osm = L.tileLayer(osmUrl, {
    maxZoom: 18,
    attribution: osmAttrib
  });

// initialize the map on the "map" div with a given center and zoom
var map = L.map('map').setView([19.04469, 72.9258], 12).addLayer(osm);

// Script for adding marker on map click
function onMapClick(e) {

  var marker = L.marker(e.latlng, {
      draggable: true,
      title: "Resource location",
      alt: "Resource Location",
      riseOnHover: true
    }).addTo(map)
    .bindPopup(e.latlng.toString()).openPopup();

  // Update marker on changing it's position
  marker.on("dragend", function(ev) {

    var chagedPos = ev.target.getLatLng();
    this.bindPopup(chagedPos.toString()).openPopup();

  });
}

map.on('click', onMapClick);
#map {
    height: 500px;
    width: 100%;
    float: left;
    z-index: 1;
    position: relative;
}

.overlay {
  height: 500px;
  width: 100px;
  margin-left: -100px;
  position: relative;
  float: right;
  z-index: 2;
  background-color: rgba(255, 50, 50, 0.5);
  pointer-events: auto;
}
<script src="http://cdn.leafletjs.com/leaflet-0.7.2/leaflet.js"></script>
<link href="http://cdn.leafletjs.com/leaflet-0.7.2/leaflet.css" rel="stylesheet" />

<div id="map">
</div>

<div class="overlay">
    <input type="radio" class = "someButton">Foo Bar
 </div>


Move the overlay div outside of the map element:

// We’ll add a tile layer to add to our map, in this case it’s a OSM tile layer.
// Creating a tile layer usually involves setting the URL template for the tile images
var osmUrl = 'http://{s}.tile.osm.org/{z}/{x}/{y}.png',
  osmAttrib = '&copy; <a href="http://openstreetmap.org/copyright">OpenStreetMap</a> contributors',
  osm = L.tileLayer(osmUrl, {
    maxZoom: 18,
    attribution: osmAttrib
  });

// initialize the map on the "map" div with a given center and zoom
var map = L.map('map').setView([19.04469, 72.9258], 12).addLayer(osm);

// Script for adding marker on map click
function onMapClick(e) {

  var marker = L.marker(e.latlng, {
      draggable: true,
      title: "Resource location",
      alt: "Resource Location",
      riseOnHover: true
    }).addTo(map)
    .bindPopup(e.latlng.toString()).openPopup();

  // Update marker on changing it's position
  marker.on("dragend", function(ev) {

    var chagedPos = ev.target.getLatLng();
    this.bindPopup(chagedPos.toString()).openPopup();

  });
}

map.on('click', onMapClick);
.container {
    position: relative;
    width: 500px;
}
#map {
    height: 500px;       
}

.overlay {     
  width: 100px;
  position: absolute;
  top: 0;
  right: 0;
  bottom: 0;      
  background-color: rgba(255, 50, 50, 0.5);     
}
<script src="http://cdn.leafletjs.com/leaflet-0.7.2/leaflet.js"></script>
<link href="http://cdn.leafletjs.com/leaflet-0.7.2/leaflet.css" rel="stylesheet" />

<div class="container">
    <div id="map"></div>
    <div class = "overlay">
        <input type="radio" class = "someButton">Foo Bar
    </div>
</div>


Another solution would be using a method, provided by leaflet it self.

var div = L.DomUtil.get('overlay'); // this must be an ID, not class!
L.DomEvent.on(div, 'mousewheel', L.DomEvent.stopPropagation);
L.DomEvent.on(div, 'click', L.DomEvent.stopPropagation);