Hello --
It is important to realise that fungus is almost always a symptom of a problem, and not the cause of one. Fungus usually attacks fish that are in some way damaged or stressed, and nine times out of ten, the cause of stress is being kept in the wrong water conditions. Mollies are the classic example of this. They need hard, alkaline water (and arguably brackish water), but when kept in acid to neutral conditions often become infected with fungus.
Now, green spotted puffers (either species) need a middling brackish water salinity; a specific gravity of 1.010 is ideal but you can go a little higher or lower without much problem. But a specific gravity of 1.005 or less is definitely not optimal, and such a fish should certainly not be kept in fresh water. Note that figure-8 puffers require a lower specific gravity, 1.005, to do well, so it is important to be sure about which puffer you have.
Another issue is feeding. Guppies, or any other kind of live fish, are totally inappropriate for this kind of puffer. While some puffers certainly are piscivores, this isn't one of them, and it should be fed a mixture of crustaceans (e.g., shrimp) and molluscs (e.g., mussel meat and snails). Food with shells still on them are essential, partly because they help to 'fill up' these puffers which otherwise seem continually hungry, but primarily to help wear down their continually growing teeth.
(I'm actually against feeding live fish to pet fish for all kinds of reasons. It's obviously cruel and has to be really bad karma, but it is also a really good way of introducing parasites and pathogenic bacteria into your aquarium. Think about how often you get whitespot in a tank when introducing some new fish. Now multiply that risk for each time you put feeder fish into the tank.)
Yes, a fungal infection could, in theory, damage the eye to the extent that the fish is blinded. But realise that the fungus only got started because you were doing something wrong. The fungus is the smoke from the smoking gun, but it's not the bullet.
Blind fish usually adapt just fine. Fish use a sense we don't have -- touch over a distance through the lateral line. This allows them to "feel" their way around very effectively at night and in murky water. Pufferfish might be an exception to this because they are very visually oriented. To be honest, if the fungus has blinded the fish, it should be very obvious. Does it react when you switch the lights on or off? Is the eye clear or cloudy?
It is unlikely that the medications -- if used correctly -- blinded the fish. There are fish/medication combinations that don't work, but they're kind of an "all or nothing" thing. For example, copper-based medications will simply kill mormyrids outright.
One medication you do have at hand is marine mix salt. If your puffer ever gets whitespot or fungus, simply adapt the fish to fully marine conditions, and voila, the pesky parasites will be gone. Kept properly, brackish water fish rarely get external infections because so few parasites or bacteria are adapted to brackish water or varying salinity.
So, here's what I'd recommend:
(1) Check your water conditions. You need a high pH (at least 7.5), and high hardness.
(2) Check your salinity. You want a specific gravity of around 1.008 to 1.012 for a small GSP, and some people keep their adult GSPs in full strength sea water.
(3) Check your water quality. Puffers are very intolerant of ammonium and nitrite, and even high nitrates (above 100 mg/l) can be detrimental.
(4) Provide a sensible diet. Puffers generally like things such as frozen krill, mysids, bloodworms, mussel, and cockle. Live snails should be offered regularly if you can get them. Some experienced aquarists believe that Malayan livebearing snails are potentially risky because they have very strong shells and could chip the beak of a puffer. Not sure about this myself, but certainly consider this.
(5) Stop feeding live fish. The puffer doesn't really need them, and the risk of bringing in pathogens is just too high.
Hope this helps,
Neale