The problem is that your regular expression matches this entire group: (as jfeoiwf) avsrv arv (as qwefo)therefore, your result.
You can use:
>>> import re
>>> line = "haha (as jfeoiwf) avsrv arv (as qwefo) afneoifew"
>>> line = re.sub(r'\(+as [a-zA-Z]*\)','',line)
>>> line
'haha avsrv arv afneoifew'
, .