Wrap Bobby in a towel for the eye drops. It was smart of you to get them to the vet right away. URIs in kittens can make them go downhill fast, so you did the right thing.

Yes there may be some reversal of trust for a little while with them, but it is very important that they get the complete treatment. You can work on trust issues again when they are done with the medicine.

In the meantime, you can help ward off too much shying away by giving them lots of attention, play time and hands on cuddling when you are not medicating them. Reach for them and hold them as often as you can between eye drop sessions, so they will not think the only time you reach for them something icky will happy.

In addition, give a special treat like a little yogurt or other probiotic after doing the eye drops, so eye drops are associated with something pleasant. They need the probiotic while they are on the antibiotic anyway.