Jessica - sorry to hear Smudge has been under the weather. I only get on here infrequently so I am not always up-to-date. Sending big {{{BE WELL}}} vibes to him.
Now about the growling, as my trainer constantly explains dogs have a limited way of telling you they don't like something, growling is one of them and it does not mean he is going to bite (especially as he was not showing his teeth), but he was telling you "I do not like this."
Look at it from Smudge's point of view. He has been quite poorly, felt unwell and probably in pain, even handling him may have been uncomfortable, then he gets in this big scary vehicle and is driven to this horrid place where they pull him around, stuff needles in him and everything smells weird and he is stressed and upset. And not all vets are the gentlest of people when it comes to handling dogs!
So this keeps happening and dog brains are very good at pairing information, it is how they learn and Shelties, as we know, are very smart. So I think Smudge has paired (going in car) with (stressful time at vets). So now he is scared and doesn't want to get in the car because, car = vets.
Well can you blame him? Imagine if it was us and someone kept shoving us in this car and driving us to a hospital where they poked and prodded us and no one explained why. We might even start to protest, refuse to get in the car - just like Smudge did.
I think if you take the stress out of the car ride, take away the association then you will see the problem of his "grumbling" evaporate. What you must not do is respond to the growling, because then he learns a growl means he gets his own way.
I think if I was you I would take very small steps with the car. First of all I would want him walking happily out to it. A few times a day I would walk him to the car and praise/reward for him approaching the car happily without fear.
Then I would just have all the car doors open (know its hard in rain) and perhaps climb in myself and encourage him to sniff about, again rewarding confidence, calm behaviour.
If Smudge can't jump in the car, I would perhaps get a ramp or make some portable steps so that he can clamber in himself - this will take away any fear you might have of him biting you when you pick him up to go in the car so you can act calmly around him.
Move on to getting him in the car and then straight out again. Build up the time he is in the car, make short trips out - even feed him in the car. Anything that will take away the negative association he has with that vehicle.
Personally, I think he is reacting out of fear and to berate him or shout at him could enhance that fear. Instead, turning the situation around to make it more positive should remove his need to growl.
You could also try going a different route to the vet. Parking further up the road and walking. Or going in a different door, anything to take away the associations.
Or you could do what I did when Cadbury became scared of the vets, though I admit it was a bit extreme - I upped sticks and changed vets completely! (Though Cadbury's fear was not the only reason).
I don't think Smudge is on his way to becoming a 'dangerous dog', but I think you need to be aware that he is very unhappy going to the vets and that he has an issue with it. Correct that issue and I am sure he will be fine.
Good luck with it all, hun. Thinking of you.