So anyway, rules loopholes aside.. some other ideas I've been toying with:
Making players actually spend actions to identify their opposition before they can obliterate them: The prime troublemakers I'm trying to keep under control are a couple of mystic adepts that have huge initiative scores. They can't LightningBall half a dozen guards if I don't have their minis on the map when their turn is up (obviously, they're going first). Make them spend the "observe in detail" complex actions to pick out where the opposition exactly is/who's a thread and who's a harmless civilian. I love this idea, but it's hard to implement without forethought about coming up with excuses about why we're putting YOUR minis on the map but not mine. Unscripted/unplanned combats make it hard to come up with such excuses on the fly.
Attack the supporting reasons that allow drain-free F12 spells: Mainly a horde of sustained/quickened buffs to drain stats. I've been shot down on the rules here on the forum at every turn. Yes, Spirits of Man may sustain 3 different buffs on you. No, mundanes can't tell you're a christmas tree of active magic without astral perception. No, you shouldn't be allowed to just use brute force to attack/break a spell/focus. No, BGCs shouldn't be all that common. Etc.
Attack EDG replenishment: Granted, drainfree F12 spells still usually involves spending EDG to reroll failures. If I'm a big mean miser about giving EDG back, I can run them out of EDG in one unimportant fight, then have the 'real' fights more as they were intended (players win, but someone besides the mages get to do something for once). Of course being a Miser with EDG is potentially punishing everyone for the mages' power imbalance.
Be a dick about collateral damage: Haven't tried it, but it's potentially a tool in the toolbox. Doesn't matter so much to destroy the NPC's gear as SRM already largely disincentivizes looting so no harm really done if nothing is lootable on the corpses. But wiping out entire buildings and so on can certainly justify handing out Notoriety and/or Public Awareness points. Thoughts on just letting a mage happily obliterate helpless opposition, but tamping down on its usefulness in this way?