How easy is it to switch the area of research in CS (going from M.Tech to PhD)?
I recently served on the TCS grad admissions committee of MIT, and I can give you my angle on things: When I'm reading applications, what I'm looking for is excellent people who strongly want to pursue research in TCS. The combination of intrinsic ability and strong desire is, in my opinion, the best way to predict success.
After all, it is our job, once someone becomes a grad student, to help them transform their potential into actual achievements, through courses, advising, etc.

Here are some important points :


Before grad school is a very early stage to change fields. Many
people shift then. It's acceptable and expected. 
In your application, explain your changing fields (so the readers understand why the rec letter writers are not from TCS, why you took lots of non-theory courses, etc). Talk about how you learned TCS, what appeals to you in TCS, demonstrate that you know the basics of the field.
If you have strong letters from your supervisors, it still counts for you, even if they are from a different field (strong = from a professor who knows you well and has great things to say about you).
If you have research experience (especially if there's some theoretical angle to it), it still counts for you, even if it's in a different field.
If you have good grades, it still counts for you, even if they are for courses from a different field. For TCS, math classes are important.