I haven't had my emails truncated by email provider [yet], but I'm all for the second suggestion (truncate the entry) on all entries. It's quite uncomfortable when the entry is long and you have to scroll to get to the comment itself. And when there are lots of top-level comments on a entry you get loads of copies of your entry.

If there is a possibility, you could make it a setting that lets users choose whether they want things like they are now or want have shorter notifications.