I understand what you're saying, and I don't necessarily disagree with you (which is not the same as agreeing, by the way: I'm just not entirely sure what the mechanics should be).
I will, however, offer a couple of thoughts on your arguments. First of all, immunity against stress suffered from drowning is a far cry from immunity to all fire. Drowning is typically a passive, environmental effect; the immunity granted by Aquatic doesn't cover "all water-related attacks". So the nearest 'flame' equivalent would be an immunity to environmental heat stress, which might cover, for example, walking across a bed of coals and such (and certainly not fireballs).
Also, Aquatic is a -1 refresh power, which (a) protects against drowning stress, and (b) allows you to move as quickly in water as you could run on flat ground. At best, the drowning portion is -1/2 refresh, so we aren't talking about a maneuver granting the equivalent of Mythic Toughness. For the -1 refresh, someone buying the power is fully as effective underwater as he is on land, granting a significant advantage against others in that environment. Permanently. For no spellcasting stress, no Fate point expenditure, etc. My suggested spell grants mere survival under water, and only temporarily, at the cost of some mental stress (admittedly not a huge cost). It requires a Thaumaturgy (-2 or more refresh) and some preparation time to do.
But I'm open to looking into other ways of handling the situation. So what do you think the mechanics of drowning should be? That might hint at a better approach; perhaps armor vs. drowning or some such.