The rise of the Incan empire rested not only on the Incas' military might and the ability of their rulers but also
they imposed a highly organized economic and political system on many different ethnic groups and permitting them to retain many of their customs and often their own leaders.
A. they imposed a highly organized economic and political system on many different ethnic groups and permitting them
B. on their imposition of a highly organized economic and political system on many different ethnic groups, who were permitted
C. because of their imposition of a highly organized economic and political system on many different ethnic groups, who they permitted
D. on their imposing of a highly organized economic and political system on many different ethnic groups and they permitted them
E. imposing a highly organized economic and political system on many different ethnic groups, permitting them
The rise of the Incan empire rested [not only] {on the Incas' military might and the ability of their rulers} [but also]
they imposed a highly organized economic and political system on many different ethnic groups and permitting them to retain many of their customs and often their own leaders.
"but also" should be followed by "on", which options B and D follows.
Between B and D, in D, on their imposing of a highly organized blah blah blah is wrong.
Hence our answer is B.