We do have some logic for catching those, it's imperfect though. The problem is that there isn't a standard email 'out of office' header so what we've done so far is to parse the subject of any incoming emails using the following regex:
private final Pattern outOfOffice = Pattern.compile("(out of office)|(autoreply)|(auto-reply)|(auto reply)", Pattern.CASE_INSENSITIVE);
We might be able to improve that a bit by also looking at the body, but if we get too aggressive (as this thread is a prime example) we'll lose messages.
The logic for this functionality lives in com.jivesoftware.community.mail.spi.DefaultIntegrationProvider, have a look if you're interested and we'd love to hear any ideas you have about making this better.