Theming of $node->body

This is a workaround, but from css .event-nodeapi { display: none; } maybe? Okay this turns of all of them, but if you have a new content-type for them, then you can hide them one-by one: lets call the new content type "event_desc", then you have to apply {display: none;} to the following classes: .event_desc-start, .event_desc-end and .event_desc-tz.

However a decent theming approach would be desirable, to have one class for the whole event box, and different ones for each type of date (start, end, tz). I will see if i can come up with a patch for it, if it is not possible otherwise.

I think you just want to override theme_event_nodeapi($node) in your theme. See Using Theme Override Functions for more information on that.