I may have misunderstood the question but:
the only difference between a and -a is a factor of -1. As long as there is another factor of both a and b that's greater than -1 (ie, all factors for 13, positive and negative are {-13, -1, 1, 13} (-1 * -13 = 13), -13 has the exact same factors. 26 would be {-26, -13, -2, -1, 1, 2, 13, 26}, as would -26, so if a=13 and b=26, the gcd of a,b and -a,-b would both be 13, because 13 > -1 > -13.