Heads of departments eventually left thank you letter (5)
I believe the answer is:
delta
'letter' is the definition.
(Greek letter)
'heads of departments eventually left thank you' is the wordplay.
'heads of' indicates taking the first letters.
'thank you' becomes 'ta' (informal way of saying thank you).
The initial letters of 'departments eventually left' is 'del'.
'del'+'ta'='DELTA'
(Other definitions for delta that I've seen before include "The Greek D (5)" , "Fourth Greek letter? - area at river mouth" , "Area of distributaries in a river basin" , "sort of wing" , "Area of alluvial deposit" .)