Yes I play a female character. Crash still appears after removing override. Removing file 003ebo.mod didn't change anything but I've done as you propose and it seems I've found a file which cause bugs, it was jorran.dlg - this file seems to change dialogs with this particular npc and I wasn't able to find others for e.g. Vrook dialog which is still bugged (maybe some files are packed together in one file). However I decided to load much earlier save (from what I hold off myself), went straight to Jedi Enclave, recruit Disciple and went back to Ebon Hawk and this time cutscene played properly. It seems that my latest saves were somehow corrupted, have no idea when or how that could happened.
About override question - I've just forgotten that some mods were installed via TSLPatcher, all have been installed correctly wihout errors.