There are two easy ways to mess with mages:
A) Increased technology. Mages suck at taking out objects with a decent structure rating or object resistance. A couple of mini-gun turrets with Redundant Processing R2 (OR = 7) will ruin pretty much any mages day
B) Counter magic: Wagemages can provide wards and counterspelling which can seriously limit (if not completely sut down) an opposing magician.
The panic room idea is solid (but expensive, so isn't going to show up just everywhere). Mages using fibre-optic links can spellcast normally (although the standard -2 dice for cover normall applies). The mage doesn't need to spend essence, but can sit quiety in the equivalent of a rigger room, and as long as every fibre optic cable is linked to every room, then the entire base is covered. This counts as an optical enhancement, which is perfectly legitimate for most Sorcery tasks (especially Direct combat spells and Mental Manipulations)
Note, this includes COUNTERSPELLING. Ergo, a mage can sit in the panic room, and provide Counterspelling dice to any target the runners are fighting.
This also includes conjuring. As the runners move from room to room, there can be a spirit summoning every time (dep[ending on drain requirements), and watchers in there warning that further violence will not be tolerated, we're watching you etc etc.
Ergo, mage panic rooms are bad.