pretty much everything ive read says that's not accurate. sense ui IS supposed to be an overlay over the android os. also, im pretty sure there are a couple of apps running around that will disable sense ui if you wanted to.
sense used be more of a skin on top, but as htc goes further and further, they seem to be going deeper into android.
i've never heard of an app that can disable sense unless you're talking about a launcher app, but like i stated earlier, they will not completely disable sense, but rather replace sense's launcher.
the only way to totally disable it is with root and a custom rom that has it ripped out.