There are many reasons why I will suggest you to go for IIT Kharagpur for applied geology and exploration geophysics. Some of these reasons include,

• Being an older IIT, IIT KGP has a much broader alumni base than Roorkee which in turn proves to be useful for higher education. 
• In case you lose interest in Core geology you are always open to sitting for non-core placements which are in abundance at IIT KGP because of the alumni network.
• The curriculum at IIT KGP is way better than Roorkee in the sense that it is rigorous and much more industry relevant than Roorkee.
• IIT KGP has good administrative support and one can get funded for conferences.
• Being an MSc course, you can avail INSPIRE Scholarship given that you have a good GPA.

These points are more than enough of a deciding factor for you.