I just changed it to set a flag in the db, which a cron then picks up and processes (essentially doing exactly what auto-payout is). Assuming your site updates are within a reasonable time, the end user experiences no real difference. They get their coins in $siteUpdateInterval amount of time.
Just one option though, I am sure there are plenty of ways to fix it.
your idea was a good one. I posted a fix in this thread: https://bitcointalksearch.org/topic/m.2533156
only complaint i have heard so far is some people want a txid immediately. i countered that mmcfe did not give it in the first place.