s/(\p{Han}+?)\((\p{Hiragana}+?)\)/\\ruby{\1}{\2}/g;

##</code><code>##

use utf8; 
binmode DATA, ':encoding(UTF-8)';
binmode STDOUT, ':encoding(UTF-8)';
while (<DATA>) {
    $_ =~ s/(\p{Han}+?)\((\p{Hiragana}+?)\)/\\ruby{\1}{\2}/g;
   print;
} 

__DATA__
This is English text with &#26085;&#26412;&#35486;(&#12395;&#12411;&#12435;&#12372;) mixed in. To test multi-furi text: &#32368;(&#12367;)&#12426;&#36820;(&#12363;&#12360;)&#12375; 
# should lead to \ruby{&#32368;}{&#12367;}&#12426;\ruby{&#36820;}{&#12363;&#12360;}&#12375;.