With a batch size of 10000 based on the original selection, no improvement.

I am going to see what sql this is creating.

         2328928 function calls (2085124 primitive calls) in 1084.925 
seconds

   Ordered by: internal time

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
       26 1074.733   41.336 1074.733   41.336 {method 'execute' of 
'pyodbc.Cursor' objects}
        2    0.871    0.436    0.872    0.436 {built-in method connect}
349128/348523    0.556    0.000    0.573    0.000 {built-in method 
isinstance}
       26    0.502    0.019    0.502    0.019 {method 'close' of 
'pyodbc.Cursor' objects}
       20    0.485    0.024    0.485    0.024 {method 'commit' of 
'pyodbc.Connection' objects}
161062/161060    0.317    0.000    0.318    0.000 {built-in method getattr}
    19123    0.259    0.000    0.789    0.000 elements.py:861(__init__)
     9567    0.258    0.000    0.258    0.000 {method 'fetchone' of 
'pyodbc.Cursor' objects}
76492/19123    0.248    0.000    2.842    0.000 operators.py:297(__eq__)
 67012/24    0.236    0.000    2.601    0.108 
visitors.py:75(_compiler_dispatch)
    19123    0.234    0.000    0.424    0.000 elements.py:2927(__init__)
     9582    0.213    0.000    1.104    0.000 elements.py:1860(_construct)
    19132    0.205    0.000    0.435    0.000 compiler.py:676(visit_column)
    19123    0.189    0.000    1.806    0.000 
compiler.py:1040(_generate_generic_binary)
    19123    0.183    0.000    1.263    0.000 
default_comparator.py:290(_check_literal)
57389/19143    0.173    0.000    2.732    0.000 {built-in method eq}
    19123    0.171    0.000    1.912    0.000 
default_comparator.py:22(_boolean_compare)
    28684    0.169    0.000    0.346    0.000 
operators.py:1007(is_precedent)
    19126    0.143    0.000    0.352    0.000 elements.py:3962(__new__)
    19123    0.129    0.000    0.795    0.000 
compiler.py:1164(visit_bindparam)
    19123    0.128    0.000    0.918    0.000 elements.py:3818(_bind_param)
    19153    0.126    0.000    0.581    0.000 base.py:1128(decorate)
        1    0.125    0.125 1084.925 1084.925 del_test.py:1(<module>)
   116845    0.121    0.000    0.121    0.000 {method 'get' of 'dict' 
objects}
38264/9581    0.115    0.000    2.567    0.000 compiler.py:806(<genexpr>)
    19123    0.113    0.000    2.048    0.000 compiler.py:1006(visit_binary)
    19125    0.113    0.000    0.174    0.000 
compiler.py:1265(_process_anon)
    19125    0.109    0.000    0.451    0.000 
compiler.py:1246(_truncated_identifier)
    19123    0.108    0.000    2.457    0.000 annotation.py:100(__eq__)
    19123    0.107    0.000    2.190    0.000 base.py:1306(visit_binary)
    19123    0.104    0.000    2.015    0.000 type_api.py:60(operate)
    38283    0.101    0.000    0.167    0.000 compiler.py:2901(quote)
    19123    0.095    0.000    0.577    0.000 
compiler.py:1233(_truncate_bindparam)
    19206    0.094    0.000    0.163    0.000 elements.py:3918(__new__)
    19125    0.093    0.000    0.323    0.000 elements.py:4073(apply_map)
    38246    0.091    0.000    0.091    0.000 elements.py:640(self_group)
    88460    0.088    0.000    0.088    0.000 {method 'append' of 'list' 
objects}
    19123    0.084    0.000    2.621    0.000 properties.py:269(operate)
38264/9581    0.084    0.000    2.586    0.000 compiler.py:804(<genexpr>)
    19123    0.082    0.000    0.732    0.000 
annotation.py:78(_compiler_dispatch)
12703/3142    0.076    0.000    2.605    0.001 {method 'join' of 'str' 
objects}
    19123    0.075    0.000    0.129    0.000 
compiler.py:959(_get_operator_dispatch)
        1    0.071    0.071 1082.250 1082.250 db_base.py:172(dict_delete)
    19123    0.070    0.000    0.089    0.000 
compiler.py:1271(bindparam_string)
    19123    0.070    0.000    2.085    0.000 <string>:1(<lambda>)
     9581    0.067    0.000    0.520    0.000 elements.py:1883(<listcomp>)
     9561    0.064    0.000    2.905    0.000 db_base.py:208(<listcomp>)
23611/23323    0.062    0.000    0.067    0.000 {built-in method hasattr}
    28705    0.061    0.000    0.159    0.000 
elements.py:4216(_expression_literal_as_text)
    28746    0.058    0.000    0.098    0.000 
elements.py:4220(_literal_as_text)
    19123    0.058    0.000    0.130    0.000 
type_api.py:504(coerce_compared_value)
     9562    0.056    0.000    0.416    0.000 result.py:1156(fetchone)
    19125    0.056    0.000    0.230    0.000 
_collections.py:728(__missing__)
    19123    0.054    0.000    0.296    0.000 elements.py:2986(self_group)



-- 
SQLAlchemy - 
The Python SQL Toolkit and Object Relational Mapper

http://www.sqlalchemy.org/

To post example code, please provide an MCVE: Minimal, Complete, and Verifiable 
Example.  See  http://stackoverflow.com/help/mcve for a full description.
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