How to react to a reviewer’s comment when he is completely right, but you do not like the consequences? One of the reviewers of my conference paper (computer science), which got a revise &amp; resubmit, criticized that my conclusions are not well founded in my experiment and that they don’t show my hypothesis. (In detail, there was no control variable, which he correctly remarked.) 

The point is, I wanted to use this experiment to give an idea for the direction of the work following my results and to generalize my previous findings. 

My question is, how could I respond to this comment, as deleting my discussion would cut out a huge part of my work?
First of all, I love the title of your question.  What an open, honest way of phrasing things, which makes for a question which just about every academic I know can identify with.

Whenever you get a "revise and resubmit" referee report, the two key questions are:


How many of the revisions do you want to make?  How many can you make in a reasonable amount of time?
Almost certainly you will resubmit, yes, but: to the same journal or to a different journal?


I take it that by "completely correct" you mean that you agree that all of the suggested revisions would improve the paper.  That still does not imply that you want to make all of them: if the revisions ask for significant further work, then it may well be that, yes, you are in the midst of this work / planning to do it in the future but nevertheless you are seeking to publish what you have done so far. 

Of course if you agree with all of the suggested revisions and you feel that you can do them in a reasonable amount of time -- e.g., in time to meet the deadline for a conference -- then it seems pretty clear that's the way to go.  

I take it though that in your case it is not practical to complete all the suggested revisions in the given amount of time.  Your remaining choices are then: (i) complete only some of the revisions, explain very carefully in your reply why you considered the other proposed revisions but did not make them, and hope for the best;  (ii) indeed resubmit, but elsewhere; and (iii) withdraw the paper until you can complete the suggested work.  Then resubmit (possibly to the same place, if applicable, but starting over again in the formal submission process).

These are tough choices, and obviously they cannot be made globally.  All I'll say is that the more (!!) "completely correct" you feel the reviewer's suggested changes are, the more likely it is that if you do not satisfactorily incorporate these changes then the paper will not be accepted.  This still does not mean that revising and resubmitting is a poor choice: you have to do an expected value computation (e.g. if you can respond to 2/3 of the suggested revisions within a few days, maybe give resubmission to the same conference a whirl: why not?) to decide what is your best option.  This decision also includes how important it is to you that the paper be published sooner rather than later and how important that it be published in this specific venue.  Ideally speaking, you should take the necessary time to publish a "complete" version of your work rather than an unsatisfactorily partial preliminary version...but in reality, many academics do not have the luxury of fully indulging this ideal.