CMI offers a more Mathematics oriented program. For pure Mathematics, it is a better option.
CMI Maths framework and teaching methodology are more suited for students who are genuinely interested in Mathematics.
In terms of reputation and scope after pursuing the course, both IISC Bangalore and CMI are equivalent. If you want to pursue a career in pure mathematics CSI offers more opportunities via better peer groups and abstract treatment in mathematics. In CMI one must take computer science or physics alongside maths and has to complete the course seriously. But if you are interested in the combination of maths and physics then you can apply to IISC Bangalore because the college is better at an undergraduate level in the teaching of science.