I really can't buy the argument that it would "screw up" game balance.
The reason being, assuming we are dealing with the post-2e vast "R&D" that WoTC added involving probability, statistics, spreadsheet analysis, massive playtest, etc., you can easily come up with formulae to involve morale. Let's say the morale check for a group of monsters is 50%. You can add that to a the equations used to measure the power of a monster and adjust based on that, just like you can take into account spell resistance or immunities into a power rating.
I think there are other reasons--design preference, etc., but not based on game balance.
The reason being, assuming we are dealing with the post-2e vast "R&D" that WoTC added involving probability, statistics, spreadsheet analysis, massive playtest, etc., you can easily come up with formulae to involve morale. Let's say the morale check for a group of monsters is 50%. You can add that to a the equations used to measure the power of a monster and adjust based on that, just like you can take into account spell resistance or immunities into a power rating.
I think there are other reasons--design preference, etc., but not based on game balance.