Eyes can be tricky - not just the injury but how the individual responds not to just the injury and it's healing but how they respond to the anesthetic, whatever is used for medication (oral and topical) and to the suture.
We had a 3 week old filly puncture her eye in/on a freshly bush-hogged pasture when she laid down and tipped over to roll. The vet decided that she needed to provide good blood flow to the eye and was hoping that that would prevent it from being "lost"... The first surgery was done w/ the wrong size/type of suture - but they were out of what should have been used on such a tiny filly and of course it was a SATURDAY. I have no idea (can't even begin to remember) what was used topically - but then the eyelid was actually "sliced" so that the inner lid could be stitched down over the eye - with a very fresh blood supply. Then the outer lid was also stitched down - to hold the other in place and to protect "everything". We then also used a topical ointment. We then applied Swat and a flyspray that we applied with a cloth applicator to make sure there were very few bugs on her face - it wasn't put where it would run into her eye....
Didn't matter - the whole thing must have been very itchy. We found rub/scritch marks all over the stall - and of course she had ripped out several of the stitches on both the outer eyelid and the inner one. The vet put her under again and restitched everything. I went home and found old nylons - instead of the fly mask that she'd been wearing that was too big and wrapped funny around her little head (not a mini, but still tiny 1/2 arab/hackney pony), we used a leg of the nylons. We just pulled it on over her head and cut holes for her ears. Also checked to make sure that her other eyes' lashes weren't "crushed" (don't remember how we actually kept the nylon from scrunching her eye). She managed not to scratch it for a little while and then opened everything again.
The new suture had arrived, so the surgery was done one more time and I guess 3x's a charm. This time the combination worked...
So - maybe try a nylon on her head? Find out if there is a different topical (there are a lot of different ones out there now) and see if that helps stop the itchiness that is causing the rubbing.
And yes, we've now been thru several eye infections and surgeries/injuries with different ponies/horses over the years. Most have healed great - one has not. Most have done extremely well with the original treatments that the vet prescribed while several had to be followed up on and other treatments tried until the "healing factor" found. That first little filly was born in 2001; has been shown under saddle on the flat and over fences; and has produced 3 1/2 shetland foals for us. She's since been sold as a children's hunt seat mount. Other than a small, blue dot where her eye was originally punctured you'd never know that she had an eye injury and most folks never even noticed that. One very serious fungal infection in our Arab mare's eye was treated with both oral and topical antibiotics prescribed by the vet and purchased at a human pharmacy - had no idea what started the infection but may have been a tiny scratch that wasn't found in time? She healed fine and is doing great now - but the treatment was "aggressive" to keep from losing the eye - it's the only time I've ever made a point of treating one so many times a day + had our daughters also doing some of the treatments so that she often got her eye lavaged and then ointmented up to 10x daily for the first 3 days. I think we literally did treatments every 2 hours - then the balance of the treatments were 4-6 x daily.
it's been two days since you first posted - how is your horse doing??
