Well, since your points are near each other, the surface of the sphere is almost flat, so just find the coordinates of the points in 3D space, so find (x,y,z) for each of the points, where
x = r*sin(lat)*cos(long)
y = r*sin(lat)*sin(long)
z = r*cos(lat)
where r is the radius of the sphere.
or something like that depending on how you define lat/long. Once you have the two xyz coords, just use sqrt((x1-x2)^2+(y1-y2)^2+(z1-z2)^2). You really can't just use a 2D Pythagorean theoreom since you would need to get reasonable 2D coordinates, which is hard.
