I think the best solution would probably be to create your own transclude-replace directive that would handle this. But for a quick and dirty solution to your example you could essentially manually place the result of the transclusion where you want:
my-transcluded-directive.html:
<div>
<span>I WILL BE REPLACED</span>
<div>I will not be touched.</div>
</div>
Directive:
return {
restrict:'A',
templateUrl:'templates/my-transcluded-directive.html',
transclude:true,
link:function(scope,element,attrs,ctrl, transclude)
{
element.find('span').replaceWith(transclude());
}
};