I'm not specifically addressing the quoting issue because, well, sometimes, it's just reasonable to consider an alternative approach.
rxvt() { urxvt -fg "#${1:-000000}" -bg "#${2:-FFFFFF}"; }
which you can then call as:
rxvt 123456 654321
the idea being that you can now alias this without concern for quotes:
alias rxvt='rxvt 123456 654321'
or, if you need to include the #
in all calls for some reason:
rxvt() { urxvt -fg "${1:-#000000}" -bg "${2:-#FFFFFF}"; }
which you can then call as:
rxvt '#123456' '#654321'
then, of course, an alias is:
alias rxvt="rxvt '#123456' '#654321'"
(oops, i guess i kind of did address the quoting :)