Did I make a mistake by choosing IIT Guwahati CSE over IIT Varanasi CSE?

It's difficult for me to say whether choosing IIT Guwahati CSE over IIT Varanasi CSE was a mistake without more information about your specific circumstances and goals. Both IIT Guwahati and IIT Varanasi are highly respected institutions, and both offer strong Computer Science programs that are rightly comparable in almost every aspect.

The placement scenario is similarly decent at both institutes with very little emphasis on research. The active Coding Club/ CSEA at IIT Guwahati gives it a slight edge over others. Both the institutes are excellent choices for whatever you want to do after graduation be it research, open source development, or a stable job.

The only distinguishing feature is the weather as IIT Guwahati has better weather conditions than IIT BHU. However, this flaw is compensated by better connectivity of Varanasi being on the mainland.