If we were discussing a machine-checked proof, then this would basically not be a problem. The correctness of an accepted proof would have little to nothing to do with its length.
Unfortunately, any proof about NP would be very gnarly and likely to be a mammoth task to formalize into a machine-checkable proof and so likely not done for a long time, if ever - the proof-checkers would be other human mathematicians. And humans are empirically unreliable. Invalid proofs have been accepted for years, decades, and even millennia (Bertrand Russell, IIRC, found a number of gaps and hidden assumptions in Euclid).
If you were looking through a program someone written, wouldn't you assume that there will be a certain bug rate per KLOC? Wouldn't you assume there is a certain bug-I-will-not-catch-reading-through rate per KLOC?
Now imagine you are looking at thousands of lines of the most fragile program ever written...
From a philosophical standpoint, I am reminded of Quine's famous attack on Popperian falsificationism - when we observe that Uranus is not on the orbit Newton would predict, we could reject Newton's laws of motion, or we could postulate some additional unobserved physical fact like the existence of a seventh planet called Neptune. Our observation has only forced us to reject the consolidated theory Newton+6-planets, it doesn't tell us which of the 2 to spare. Similarly, when our potential proof finally terminates in a contradiction, all it tells us is that somewhere we went wrong; it doesn't tell us which axiom or theorem we ought to throw away as false.