Will addressing reviewers comment and accepting drawback of work take back my acceptance? Recently I got a paper got accepted by a well-known conference (computer science). I am about to submit a camera-ready version of the paper for the conference proceedings, trying to incorporate the comments of the reviewers.

Two out of five reviewers point a problem in my research design, which is something I have felt too, but didn't weigh in much to address at my paper. Now, before submitting the camera-ready version, I feel that I should address the opinion of the two reviewers, but that would come up as a major drawback of my research. If I do so, what are the chances that it will have a negative effect on further publication? 

I am new to academia and don't have appropriate advising regarding what to do regarding this.
In general, if you got an acceptance notice from a conference, then you are accepted.  At this point, it's up to you just how much to take the reviewers into account in revising your paper. 

Personally, I do recommend changes in response to every issue raised, because that will generally make you paper stronger.  Even if a reviewer is dead wrong, it at least points to a place where readers can become confused. In this case, kudos to you for taking the reviewers seriously and thinking carefully about their feedback, rather than just being defensive.

Note that in some cases you may get a "conditional acceptance", and in that case you definitely have to be concerned about the reviewers' opinions of your new version.  That does not seem to be the case here based on what you have written, however.