Sometimes ya gotta do what you gotta do! And it's better for him if you do it than if you don't and he gets a ton of infection. (You might want to add either some cranberry (capsule) to his diet or even some D-Mannose -- both of those are largely glucose which bonds to infection cells so they don't 'stick' to the urinary tract... it might help prevent infection. Won't do a thing to prevent crystals (altho the vet should have told you to stick to probably an acidic diet ?? depends on whether they are thinking struvite crystals which are most common and are found in urine too alkalyne or oxalate crystals which tend to be in acidic urine -- it's FAR more common for a dog's urine to be too alkalyne, not too acid. Their PH is different from ours.)
As long as you don't rush and push overly hard you should be quite safe. Many folks have to do this on an ongoing basis for a dog with spinal issues.
He probably doesn't enjoy this any more than you do -- praise him a lot when he TRIES to go and he should continue. Let him know he's doing GOOD and encourage him to keep trying.
It gives HIM relief too -- so just keep it low stress and keep letting him know that him trying is doing a GOOD job. "And let's see if we can help you get some more out of there ..." You don't want him to think he's 'failed' you just want him to know you're helping him.