Throw out rogue initially seen in storehouse (6)
I believe the answer is:
deport
'throw out' is the definition.
(deporting is a kind of throwing out)
'rogue initially seen in storehouse' is the wordplay.
'initially' suggests taking the first letters.
'seen in' indicates putting letters inside.
'storehouse' becomes 'depot' ('depot' can be a synonym of 'storehouse').
The first letter of 'rogue' is 'r'.
'r' going inside 'depot' is 'DEPORT'.
(Other definitions for deport that I've seen before include "Expel from country - not a citizen" , "Expel to another country" , "Exile" , "Banish (undesirable alien?)" , "Send home" .)