The script:
#!/bin/sh
echo args: $*
echo pwd: `pwd`

Run from a nautilus window in /tmp with two files selected outputs:
args: file1 file2
pwd: /tmp

So, I don't see this.

Clarification: I'm not talking about Nautilus scripts in ~/.nautilus/scripts,
but my own scripts I have elsewhere.  These are always run in $HOME regardless
of where the script is located.

How would you distinguish this from double clicking on a binary
in /usr/bin? Would you want to run them with /usr/bin as
the cwd?

I feel that executing binaries with the homedir as cwd is probably the right
thing to do. Therefore i am marking this as WONTFIX.

If you disagree, please bring this discussion up on the nautilus mailing list.