Did your mother make you take absolutely awful tasting cough syrup......mine did.......or take you to the vet....I mean Doctor......who gave you shots and such.....mine did.....did it destroy your relationship? No.
We have to give Marli eye drops three times a day right now...and these are required to be kept refrigerated. She is trying new ways of twisting, shutting her eyes, everything....each time to avoid them. I am very sensitive toward my eyes and know how I would hate the cold drops hitting. Its hard with a kitten. However, we just have to hope that we have built a trust relationship that she hates this act but still loves us. And, from experience, it does work out that way.
As to your cat starting to run when you come near him......just go near him more often than ever without medicine and pet and cuddle him. Also, after the drops, I continue to hold and pet Marli a bit and then give her the promised treat. She certainly doesn't run. In fact, once I put her in the floor, if I am too slow with the treat...which I generally am according to her....she does let me know she needs me to hurry up.