It is a little awkward that you do not mention what compound this is about but I guess you can't be forced to tell... because right now there seems no reason for this to be in the PD forum and ADD seems more suited. It is kind of basic (no pun intended), but I think that it just might be a bit too much for BDD.
Anyway if this works depends on what your compound is, how polar or not. GAA is a good protic polar solvent for a number of things, yes. Maybe you know this and find it nitpicky but if you use the GAA to dissolve your compound it will only really be a salt if you get it out of the acid again. It will be ionized but in equilibrium in the time the compound is dissolved. So how were you planning on isolating your compound from the GAA? You say normally it is extracted from the aqueous layer. Oh yes? How?
What is the point anyway of doing this, why not just dilute your acid in water? Are you worried that it is not acidic enough to protonate and extract the freebase? You can check the protonation constant for your compound, the 'K(a)'. It is the pH at which 50% is protonated. If this value is very low that means to salt or protonate your compound you need a very low pH, even a bit lower than that value.
Having two liquid phases makes the dynamics more difficult though, because when shaking them the freebase that is protonated goes into the polar layer. So it's a bit complex to talk about the Ka since the apolar compound simply has no pH. But what it does mean is that the % of compound in the acidic layer that is not protonated in the equilibrium has a tendency to go back into the apolar layer again... pffffff
Whether your compound can be burned depends on what compound it is. For charring like sulfuric acid on wood, that sort of burning... no I don't think that most organic compouds would oxidize like that in GAA. But they can if there is an acid-catalyzed degradation reaction that your compound can be in.
Acetic acid is a relatively weak acid but GAA is indeed corrosive - but mostly to metals and and stuff like that.
Anyway I see no reason not to just use diluted acid water, and if possible muriatic acid (HCl) because that can evaporate okay. With your protonated compound in the watery solution you can evaporate it to yield your salt. Though this sucks if your compound is hygroscopic. Then you will have to use vacuum or a desiccant that is more hydroscopic than your compound.
