Departs in good time but at great cost (6)
I believe the answer is:
dearly
'at great cost' is the definition.
(synonyms)
'departs in good time' is the wordplay.
'departs' becomes 'd' (common abbreviation e.g. train timetables).
'in good time' becomes 'early' (being early is arriving in good time).
'd'+'early'='DEARLY'
'but' acts as a link.
(Other definitions for dearly that I've seen before include "At high cost" , "At a high price - with fondness" , "With affection - at great cost" , "How I love my wife" , "Very much; at great cost" .)