What? You wanted me to answer the question? : )
You're right, it won't help with that, although if you're trying to hide the technology map viewer, you're probably just as interested, if not more, in hiding the source. So the .qxp helps with that, but I'm sure it's still visible in the technology map viewer. (Note that, since the viewer is purely graphical, you're relying on someone redrawing and reverse-engineering the entire thing. If it's a few thousand logic cells, I imagine that would take a few weeks. I've done schematic conversions by hand, which is much easier, and it takes a LONG time, assuming you don't go crazy first. A simple schematic page can take 2 hours on average, so a twenty page schematic takes a week. That's not fully taking into account the typos, unhooked wires, etc. that need to be debugged.
But in the end, it's do-able. Altera does provide way for vendors to protect their IP, although I don't believe it's in the general release, so you'll need to contact Altera(field office or apps via SR) and discuss your situation. Maybe someone that has more details can chime in.