edit: Oh crap, just saw you've solved your problem already!
Since you're asking about a simple app, what follows may not be very helpful to you; but anyway -- I'll try.

Pro Motion by Jan Zimmermann/Cosmigo (look up Google) is a really wonderful software, and it handles alpha layers within .PNG files. One problem is that you'd have to carry an additional mask-or-something file with your .PNGs, which is not a comfortable option considering its pragmatic usage in games.
Anyway, it sure IS possible (using some coding magic) to have one color in an indexed 8-bit .PNG that is 50% transparent. You might ask a coder, or anyone in your team who handles programming to look closer at the matter, since it would probably take one.
I'd suggest converting to .GIFs, then. :/