Yes, you can discontinue M.Tech Course at Anna University to Join a IIT, but the issue lies whether you have to return your M.Tech Stipend or Not.

So, according to AICTE you will require returning the M.Tech Stipend if your discontinue your Course. However, if your Institute is being funded by the MHRD, you need not require returning the Stipend.

Better, You must Check the details with your Institutes Regulatory Authority.

I believe, unless you do not require a Transfer Certificate for Joining M.Tech at IIT, you may not go through the official procedure of Course Discontinuation at Anna University, and you will automatically be striked off the list from Next Semester, due to Non Registration. However, in case you need a Transfer Certificate, you may require informing the Registrar of Anna University, and hence return of Stipend as well as the Official Procedure.