A few comments.
1. He's just saying he's unhappy. As long as your are doing the injections properly (in muscle) and not hurting him, it's fine. I got Yafe, my Carpet Python, after being lost by Fed Ex and he developed a serious RI within 24 hours of arrival. He wasn't happy about the injections, but my wife and I were as gentle as we could be and did our best. I spent a minute with him after injections basically letting him calm down and then putting him back. I did not handle otherwise during treatment.
He will not hold a grudge and you have plenty of time to change his mind after he's better.
2. You said the vet diagnosed an RI with a blood test? That's not good. In order to properly treat an RI, a tracheal wash should be done so you know what type of bacteria and therefore what antibiotic to use. You will also know if it's not bacterial (which can happen - viral or fungal can happen as well).
At this point, finish the antibiotic and hope the vet guessed properly. However, find a new vet.
3. Make sure the cage is clean, clean, clean, and temps and humidity are perfect.
You did not say how he got the RI, but proper husbandry will only help him heal and prevent another infection. Depending on type and severity, RI's can make a snake more susceptible to another infection.
Finally, if you have questions, don't be shy, ask. We are here to help.
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