You have a couple options here.
First if possible (I know you mentioned it's an ASCX hierarchy, but you can make individual transformations either text/xml or ascx, you can mix and match) is to utilize K# (text/xml transformation type), in it you can use the following macro to transform:
DataItem.ApplyTransformation((parent.booleanValueIsSet ? "Custom.MyTransformationName1" : "Custom.MyTransformationName2"), "ContentBefore", "ContentAfter")
If you MUST use ASCX, then you can either reference the CMS.MacroEngine.MacroContext.CurrentResolver.ResolveMacros() method (passing it the same k# macro above, although not sure if the DataItem will be available, it may), or you may need to put a Repeater control in your ASCX transformation, then use a server script to dynamically set it.
<cms:repeate runat="server" id="MyRepeater"/>
<script runat="serve">
public override OnInit() {
MyRepeater.Path = Eval<string>("NodeAliasPath");
MyRepeater.TransformationName = (parent.booleanValueIsSet ? "Custom.MyTransformationName1" : "Custom.MyTransformationName2");
}
</script>
I would get the exact code, but right now i'm VPN-ed out of my wok computer with the sample, so if you need me to post it just tell me, otherwise i would go with the macro method!