If I understand, you start with a solution of KOH in butanol, run the reaction and add H3PO4 and have a solution with H3PO4 and salts - all in solution in the butanol. Even at 0.1 M, I would not put this into a GC system if I could avoid it. If you must do this, use a GC inlet liner with a large plug of glass wool - there is at least one type that has a plug at least 1 cm long. And be ready to change it frequently. Run a check standard with analytes of interest (but no phosphates) every few samples until you get a feel for how long you can go between changes of the inlet liner without getting poor results from an active inlet.
I'd rather get the salts out of the solution before making the injection. And partitioning into water is a good way to do that -- assuming your analytes will partition well into the organic phase.
Getting a clean separation that clearly separates water from butanol is tough. But you may be able to take a mL of your reaction mixture and partition it between 20 - 50 mL DCM and some water. Alcohols should be recovered largely in the organic phase and - assuming you are reacting suffient ester in this mixture, you should have strong enough peaks to get a good trace on the GC without introducting salts into the GC inlet.
Ion exchage can be used to get rid of both anions and cations - but without further information, there is the consideration of loss of analytes to the polymer that makes up the resin. If you want to go in the direction of a column separation, I would look at SPE, where you would wash away the ions with water and then strip organics from the column/cartridge with a solvent that would go nicely into a GC.