Poor users, Kayako will never have the brains of a human
The method we use is that the staff user of department A creates a new ticket on department B they use the staff cp rather than e-mail. This prevent the mail parser adding post to the original ticket. If the staff user sets their own e-mail address as the ticket user, then the correspondance can continue via e-mail.
We call the process 'parent' and 'child' tickets. There is also a custom field for each ticket where the appropriate parent/child ticket id can be recorded. This allow staff to easily find the original source conversation with the customer.
Hope this gives some ideas or apologies if it doesn't relate your scenario,
Rob