HTML5 Video showing both Source and Flash fallback
In these kinds of cases, the easy fix would be to add a second text field for "embed code" outside the main wysiwyg area. If you set it to use a new "HTML without linebreaks" text formatter, that'll help eliminate any wackiness on the "Full HTML" default setting.

Protip: use the Better Formats module to stop the user from having to choose a format for this field. That way, they can just paste and forget.