Recently I found a php script by Chris Morrel which allows you to post photos to flickr (and get the correct flic.kr short url back) from Tweetie 2. I tweaked it a little to get used hashtags as flickr-tags and to have them removed from the title (the script uses the message as the title).

Right after:

$tags = FLICKR_TAGS;
if (TAG_WITH_HANDLE) {
$tags .= ' @' . $_POST['username'];
}

I added:

preg_match_all('/#(\w+)/', $title, $matches);
foreach ($matches[1] as &$tag) {
    $tags .= ' ' . $tag;
    }
$title = preg_replace("/#\w+/i", '', $title);

It worked as I wanted, so yay!