Unfortunately these sort of bugs are the ones that happen when using an SMTP server directly (I believe its mentioned in the caveats somewhere). Easiest solution is to configure it to use a local postfix which forwards to mandrill.
As mentioned in my first post, not the sending of emails is the problem. This is done in batches. The problem is the queueing of emails in the db. This process is the same for every delivery method and should also be done in batches.
The same potential issue happens with threads/posts with thread/forum watching. Unfortunately, we don't really have a great general solution for this. This is something we may need to look into for a future version.
A possible partial workaround involves limiting to only attempting to contact people that have been active on the forum in the last X days. (On the assumption that if someone hasn't visited in months, they're unlikely to come back but that may not be an accurate assumption in all cases.)