All but one of my girls have let me scruff them without too much of a fight, but it's not something I've ever done on any sort of regular basis, and definitely not for medicating. You're just asking for them to hate being medicated at that point. Nothing is more of a pain than trying to get meds into a rat who is really fighting you. Plus, it's never helped me medicate them any easier, or do anything else to them, for that matter.
If your vet, or you, are that concerned about you having difficulty getting their meds into them, ask for a higher concentration. It will always be easier to get .05cc into an unwilling rat than .20cc. When my rats are really unwilling to take their meds [which hardly happens since I switched to Baytril pills], I sit down, hold them against my stomach with their body laying up my chest. Hold them with one hand over their shoulders, pop the syringe into the side of their mouth and squeeze the plunger. It literally takes longer to adjust their position than it does to get the meds in. Make sure you're wearing a shirt you don't mind getting sticky meds on, too. I only do this with small amounts of medications. I'm not comfortable with doing this method with more than .10cc tops, so if your vet won't concentrate your meds more, I would suggest doing it in a couple of sessions [or one after the other if your rat will do it] so there's no risk of aspiration.
Lots of people do this instead of trying to mix meds in with "goodies" to try and tempt the rat to eat them. There's a thread dedicated to just what all you can mix with meds to try and get them to eat it on their own.