The top 3 answers to the MathOverflow question Which mathematicians have influenced you the most? are Alexander Grothendieck, Mikhail Gromov, and Bill Thurston. Each of these have expressed serious concerns about the community.

Grothendieck was actually effectively excommunicated by the mathematical community and then was pathologized as having gone crazy. See pages 37-40 of David Ruelle's book A Mathematician's Brain.

Gromov expresses strong sympathy for Grigory Perelman having left the mathematical community starting on page 110 of Perfect Rigor. (You can search for "Gromov" in the pdf to see all of his remarks on the subject.)

Thurston made very apt criticisms of the mathematical community in his essay On Proof and Progress In Mathematics. See especially the beginning of Section 3: "How is mathematical understanding communicated?" Terry Tao endorses Thurston's essay in his obituary of Thurston. But the community has essentially ignored Thurston's remarks: one almost never hears people talk about the points that Thurston raises.

Just a quick note on your main example - in math, and I'm guessing in theoretic areas of CS as well, we often find that searching for fundamental obstructions to a solution is the very thing that allows us to find the solution. This is true for a number of reasons. First, if we find no obstructions, we are more confident that there is some way to find a solution, which always helps. Second, if we find a partial obstruction to solutions of a certain sort, we learn something crucial about how a solution must look. Third, and perhaps most importantly, when we seek to find obstructions and fail, we may find out way blocked by some kind of obstruction to an obstruction, which is a shadow of the very solution we seek to find, and by feeling it out we can find our way to the solution.