I am careful about structure and detail of designing scenes instead of encounters.
So if a foe is getting "great dice" then it means "that isn't just a goon, that is Super Goon the Ultraminion!" and now he earns a name. He will try to fulfill his goal in the scene and escape with his life, just like everyone else. Maybe a character/npc/monster is crestfallen, ill, bad day, bad karma, whatever. I like to prod the player - "Why is your character getting these bad rolls? Is this just bad fortune, or an off day, or perhaps fate seeks to bring you down?" - I like to let the player have some fun with the fact that the dice are "being odd".
Reminds me of Axis and Allies, I had a friend that every time we played, he would make a big attack and roll 5's and I would roll all 1-2's and he would be so mad.
There are other ways to lighten things up than misusing the advantage/disadvantage system. I would also be careful in your wording, as abuse and misuse are very different on terms of foul play and malign nature. I would say you are misusing the system for a good motive, but you are still having a negative impact. If a monster gets a few big shots off, be ruthless, have it sneer and spit or do something else to signify that "this ain't no ordinary zombie by the lake in a hokey mask". Or if the player easily defeats an enemy, let the enemy be not only defeated, but defeated utterly and spectacularly - that will maximize the fun, and create an "oomph!" moment which gives you the time to make a brief plot adjustment.
"My intended miniboss was killed in advance. Got it. Enemy scout gives the actual boss a message, who commissions someone else to "do it instead". The PC's should maybe be given 1-2 tales of the easily defeated character's glory - "That wizard you just beat once killed a storm giant that attacked this city..." or "I feel bad for the knight you beat. After the plague took his wife and sons, he became a drunk and hasn't been the same. Gods have mercy." This just adds a layer. I like to find ways to add layers all over the place. Seeds now which might or might not matter later.
If an NPC accidentally "steals the show" with a good performance, that is usually how NPC's earn a name and go from "that knight you hired" to "Bryant of the Red Apples".