Python's grammar is such that negative integer literals don't exist; what you actually have there is the unary minus operator applied to positive integer literals; ...
Well, knowing that there are more negatives than positives and then coding it this way appears in fact as a design flaw to me.
Don't know what you're saying here. Python's grammar has nothing to do with the relative number of positive vs negative entities; indeed, in a 2's-complement machine it's not even true that there are more negatives than positives. Python generates the unary minus for "negative literals" because, again, negative literals *don't exist* in the grammar.
A simple solution could be to do the opposite: Always store a negative number and negate it for positive numbers. ...
So long as negative literals don't exist in the grammar, "-2147483648" makes no sense on a 2's-complement machine with 32-bit C longs. There isn't "a problem" here worth fixing, although if there is <wink>, it will get fixed by magic as soon as Python ints and longs are unified.