Acceleration has everything to do with the capabilities of the machine. Meaning how rigid it is. High acceleration rates will keep the tool closer to the real path when constant velocity mode is used. However, if the machine is not capable of using the higher acceleration rates WHILE cutting, then the acceleration values need to be lowered (as you have noted). So if you are wondering or waving on a corner, it is most likely machine flex going on.
So on to how to solve this... One could implement a custom M code (or two) to raise and lower the motor acceleration values. Using the mcMotorSetMaxAccel() API function. But I suspect that doing some reading up on CV tuning is what will help you the most. There is a CV tuning wizard that will actually let you control how fast the machine goes into and out of corners, etc... Slowing the corner speed may allow the higher accel rates to not impact the cut quality.
Steve