It is hosing him if blasting his foes to smithereens has absolutely no effect on the combat. In fact, the controller "killing" minions has a detrimental effect on the outcome, since he has spent an action "killing" minions that he could have spent debuffing a bad guy, or just chipping in his magic missile damage. "Killing" in quotes there because all he really did for all his effort is teleport them just off the battle map for a round. And you don't have to tell him, he just has to have the intelligence of a slightly dim turnip to eventually realize that every time he fires off his Stinking Cloud or Flaming Sphere, well gosh and golly, there's a second wave of minions. But when the ranger kills them one at a time, no second wave. Wonder why that might be? And about that time the wizard charges into melee with the dragon and the player decides to make a striker for his next character.
What do you mean, no effect?
Look, there's a bunch of bad guys. BOOM! The wizard makes them asplode! Now there's a lot fewer bad guys. And its a good thing, because here comes EVEN MORE bad guys! Man, its a good thing the wizard asploded all those guys, because if he hadn't, we'd be completely outnumbered!
These are basic DMing skills 101. When you have an encounter that is of a type you know your PCs aren't well equipped to handle, you lower the difficulty. When you have an encounter that is of a type your PCs are extremely well equipped to handle, you increase the difficulty.
And when your PCs have an ability that's really powerful, and that really blasts through an encounter of a particular type, you have two choices. One's good, and one's bad.
The bad choice is to nerf the ability in some way. This can be done by either making up circumstances where the ability can't be used (in 3e, this is the clumsy anti-magic zone answer to overpowered spellcasters), or simply never using the sort of challenge the PCs easily overcome.
The GOOD way is to embrace the powerful ability. Balance the encounter so that after the PCs use their particularly powerful ability, a balanced, fun encounter remains behind. A 3e example of how to do this is my answer for Turn Undead. Turn Undead can really toast an encounter in 3e, if the cleric in question has invested feats in improving it, and has the right ability scores. It can actually render an entire fight moot, or ruin the challenge of a climactic battle. What's the solution? Well, you only get so many Turn Undeads per day. And they always destroy the weakest undead monsters first. So, I simply make sure that, when the climactic battle arrives, the number of weak skeleton and zombie minions is calibrated to match the number and strength of the cleric's remaining Turn Undeads.
Why is this a good solution?
Because the cleric gets to feel like the ULTIMATE BADASS! They walk into the room, and there's like THIRTY SKELETONS AND ZOMBIES milling about! Behind them there's a skeletal dragon, and a necromancer controlling them all! And the cleric called out to his god, and just, BOOM! The skeletons and zombies started melting into dust before the holy light of his god! A few short moments later, and there's a clear path right through the now demolished throngs of undead, and the fighter and ranger are charging the terrified looking necromancer, who's reaching for his tome of magic in a last ditch effort to save himself from righteous vengeance!
Now, look, obviously you can't TELL the cleric's player what you did. That wrecks it. But D&D is always like that. You can't TELL the pcs that the reason they didn't find anything particularly amazing in the necromancer's treasure is because they came up with that really good idea last night that got them all that high powered treasure, and you need a few short nights to rebalance things. You can't TELL the pcs that the challenges they face have subtly changed because previously they had a Bard in the party and now they have a Rogue.
There are lots of things you can't tell the players. That's how it goes. It doesn't mean those things are bad.