Your system is interesting! I'm not sure I will remember the math enough to do it quickly on the fly. If I have it right, you figure the difference between the enemy and the PCs, and if the PCs are higher level you subtract the difference from the save DC, and if the enemy is higher level, you add it? But then it's a straight wisdom roll to beat the DC?
The math isn't too bad, and frankly I know 99% of the time since CR vs. Level is often within 5, for the most part a roll of 15 or better nearly always makes it and a roll of 5 or less pretty much will always fail. However, I have the CR listed for each encounter in my notes, so the math isn't too bad for me, personally.
Yes. PC higher level, subtract the difference... the creature is more likely to flee when it gets beaten down (often quickly) to half HP. PC level lower, add the difference... the creature is less likely to flee since it is stronger and likely is giving as good as it takes.
After that, base 10 DC and straight Wisdom check (not a saving throw like 2014 DMG says!!!).
What do you do for groups of enemies? Say your level 8 PCs are attacked by a gang of level 5 bandits, and the bandits outnumber them. Do you treat each individual bandit the same as the single Hill Giant, or do you make any modifications for having numerical advantage?
I generally use the adjusted XP value for the encounter and determine an encounter CR. In a recent encounter I had 10 quicklings (CR 1) worth an adjusted XP 5000, making them a CR 9 encounter. So, the base DC is 11 vs. 8th-level PCs.
I make checks on the first death, at half strength, and if there is a clear leader, whenever the leader is defeated.
In the quickling encounter, a PC dropped first before a quickling, and frankly it looked bad for the PCs. So, when a quickling dropped I made the check with disadvantage--the quicklings were "winning" clearly. IIRC the low roll was a 6, so +1 WIS mod for the quickling totaled 7, failing vs. DC 11. The quicklings pressed the attack.
Later, when two PCs were hasted, and started killing quicklings, I made the check when 3 were left. I would have made it at 5, but the PCs killed two before the quicklings turn happened. At this point, it looked bad for the quicklings as their speed was not helping as much, so I made the check with advantage and easily beat the DC 11. The 3 remaining quicklings fled successfully (120 feet speed helps!).
If this sounds too complex it really isn't for me because I do enough prep work for encounters I generally know the DC with a glance at the encounter CR. However, you could do a base 10 DC and then +/- 5 for the difference in tiers between the party and the creature. Or, simply make it advantage on the check if the creature is lower CR (it will likely flee so you want to roll high) and disadvantage if the creature is higher CD (it will fight because it believes it can win).
There are really lots of ways to handle morale that can work--it just depends on how complex you want it?