It's possible, but not with a template, because <iframe/>
's will be removed.
Modify the infoWindowHtml-property of the FusionTablesMouseEvent
google.maps.event.addListener(layer,'click',function(e){
e.infoWindowHtml+=
'<iframe width="100%" src="https://www.google.com/fusiontables/embedviz?'+
'viz=CARD&q=select+*+from+childTableId+where+ID+%3D+'+
e.row.ID.value+'&cpr=1"></iframe>';
});