I agree with @aprilk about trying to create as positive a Vet experience as possible especially for a young dog. I also get that's not very doable without being able to be with her. I liked the idea of asking if an examination outside (in front perhaps) of the office might allow you to be with her. Even if you did decide to muzzle up, she'd still have you right there giving her reassurance during the exam and a favorite snack right after. I'd definitely be asking the vet for a little extra help/effort on this issue.
Jengo was always terrified going to the vet. My vet and I talked about it and she always gave him special treatment like not putting him in a crate, allowing him to roam free with the vet techs. I always brought the team cookies, chocolate, or another treat as a big thank you for the extra effort.
I suppose an argument could be made that that's what I'm paying them for, why should I have to do cookies too? I love my doggies. I want everyone who has a hand in their visit to be invested. Logan and Sparkle went in for the first time (while with me) on Monday for hip x-rays; eye, ear, nose and mouth exams, blood tests, etc. They came home a bit groggy, but happy... and with trimmed nails, which was cool! Everyone got a treat that day.