AviK, suppose I have a mezuzah up on my door, and I know what it says and am constantly thinking of it, but there’s one little problem: it’s possul. One letter is missing, or there’s an extra letter, or a letter is malformed, or has split, etc. Leshitoshcho, why does it no longer protect me? Why, when we have problems, do we check our mezuzos and tefillin, to see whether an unknown psul might be responsible? After all, you claim it’s not the mezuzah, or even the mitzvah, which protects, but only the kavanah, and my kavanah can’t be affected by a psul of which I’m not even aware.
This proves that it’s not the kavana but the mezuza itself (or the mitzva of putting it up) that protects. If the mezuza is possul then no mitzva has been done, despite the greatest kavonos, and therefore the promised protection doesn’t come. And of course whatever protection comes from the physical mezuza cannot come from a posul one.