What about forward references? Can you use definitions before they occur? If not, it seems like you just need to do things in one pass instead of two (untested):

.
.
.
my %defines;
while(<FILE>) {
    chomp;
    if (/^#DEFINE \s+ <(\w+)> \s+ (.*) $/x) {
        my ($def, $text) = ($1, $2);
        1 while $text =~ s/<(\w+)>/$defines{$1}/;
        $defines{$def} = $text;
    }
}
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.
.
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And I hope you're only calling this once per file. If you pass in the same filename multiple times with different $options, then you should be caching the definition maps in a global variable or a passed-in parameter, like:

sub parseDefines {
   my ($filename, $option, $defines) = @_;
   return $defines->{$option} if $defines;
   $defines = {};
   ...
}
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