While possible to kill a noble, they typically have stuff like knights with them, along with most people they go after not being in a position to retaliate easily, making that very unlikely. Plus, they tend to do stuff like killing the friends and family if you resist, making people far less willing to do so. People in power have always found plenty of ways to make their targets afraid to retaliate, and the very miniscule possibility of successful revenge from peasants in a medieval fantasy settings is barely even a factor.
As for revolution, while that is true, giantesses being in charge does help stop bad changes in government as well. There are plenty of times in fantasy stories that a decent ruler gets killed or replaced by a worse one, leading to countries becoming worse off. There are times when new bad people end up overthrowing good ones, so it's not entirely a good thing to have more vulnerable governments. The giantesses being split into their kingdoms with the guardians are far more stable in that regard, so good kingdoms tend to stay good while bad ones tend to stay bad. Heaven kingdom and the Queen's place will pretty much always stay good places to be, while Homaspernia will always be awful. If giantesses were gone, whether the new kingdoms that sprouted up afterwards would be overall safer or not would be purely a matter of writing, and it could change very frequently whenever the rulers do.