Beer-covered theologian Darwinism initially confused (6)
I believe the answer is:
addled
'confused' is the definition.
(addling is a kind of confusing)
'beer-covered theologian darwinism initially' is the wordplay.
'beer' becomes 'ale' (type of beer).
'covered' is an insertion indicator.
'theologian' becomes 'DD' (Doctor of Divinity degree).
'initially' indicates taking the first letters.
The initial letter of 'darwinism' is 'd'.
'ale' enclosing 'dd' is 'addle'.
'addle'+'d'='ADDLED'
(Other definitions for addled that I've seen before include "Rotten; muddled" , "Completely confused" , "Befuddled" , "spoiled" , "Confused like rotten egg" .)