Mine was similar. He had an op on his elbow. He refused to eat his antibiotics at home and his stitches burst. So he went back to the vets for a week. He was being injected twice a day and became so unmanageable he was sent back home again!! They had to put him in the stalls for any chance to get the needle in, but he was messing about so much his neck was getting bruised so he just associated everything with pain. They managed to source other oral abx which luckily he ate.
However I was then left with a needle phobic horse. I had to go right back to the beginning as even touching his neck had him freaking out. Slowly slowly until I could raise the vein without issue and then used a pen to touch his neck. Of course it took time which you may not have now. But lots of work going through the motions without injecting. Also those little mollases licks. They are full of sugar and not something he would normally get so bribery works. Initially when vet came I would shove one of them under his nose and he would put up with him. Glad to vet had injection done before I had “prepared” this week and he didn’t bother.
If he really needs abx and you really can’t get them in the only other way is to take him to horspital and put in a catheter in neck.
Another way, which isn’t ideal but needs must sometimes, is reverse him up to stable door. Someone holds his head and distracts. Someone comes over door and puts jab in bum. It saves you from being kicked.