A lot of people seem scared about the Wish spell. In my games what I do is allow the effects detailed in the spell text but ignore the "GMs discretion" part. I think that solves most of the problems.
Greater effects are disallowed in my games because I don't want to create a precedent that players may exploit in the future and may not be appropriate to the situation they are in. If a greater effect is possible, I will tell them. Sometimes they ask for something specific.
As an example, last session my players wanted to go up the wormvent in the tabernacle (they had defeated all the enemies) but didn't want to suffer the blood of kyuss effects. They knew their best option was to use a etherealness spell and go up (the blood, unlike the worms, doesn't manifest in the ethereal plane) but unfortunately neither the cleric nor the solar ranger had prepared it.
I told them that if they used a miracle, I'll allow them to reach the upper wormvent. So the cleric casted it and her deity surrounded them with divine energy to let them travel to the wormvent's bottom (they saw all the worms feasting on each other inside the cavern) and then all the way up to the worms' path entrance.
Another example: They discovered the hidden lashonna ring in Venk's parlor. After activating it without thinking too much, they found themselves inside a magic circle in Lashonna's dungeon. Thinking that they had screwed up, the players asked if they could use a Wish to escape back to the tabernacle, and I allowed it.
As for Balakarde's buffs, yeah they go away once dragotha is dead as Balakarde finally travels to the afterlife.
Hope this helps.