The code you wrote counts the number of polygons being disjointed from every point, so assuming the points are in only one polygon, you can expect to find a count of
number of points * (number of polygons -1 ).
If you want to count the number of points being disjointed from the entire layer, i.e. from ALL polygons, you would need to do the opposite: discard any point that intersects at least one polygon, and record the ones that do not intersect any polygon.
Using your code, it could be modified to the following. Note that there is probably other (better) ways to do it on the entire layer directly.
for pointFeat in layer1.getFeatures():
intersected = False #reset the boolean flag
for polyFeat in layer2.getFeatures():
intersected = True #point and polygon do intersect
break #no need to check other polygons
#Now that every polygons have been tested, deduct if the point is disjointed or not
if intersected == False