my @args = map { ($_, foo($arg{$_})) } keys %args;

# either: prepend \ to all $ in @args
s/\$/\\\$/g foreach @args;

# or maybe: quote all single quotes, then single-quote all args
s/'/\\'/g foreach @args;
@args = map "'$_'", @args;

my @output = `/bin/foo @args`;