It will go down to the question, which of the two procedure can be done the quickest.
Although holding them upright and injecting them would give them stress it will just be for a brief moment.
Unlike holding them like a baby and then injecting it subcutaneously, holding them everyday, it means you are giving them stress everyday, because you need to catch them before you can hold them. They would run, jump etc. once you have hold them you will try to accustom them to be hold like a baby. But for sure they will have resistance and this will also cause stress.
Assuming, through that process they are now at ease at you holding them like a baby , once you inject them , they will have a recall of the event. Everytime you hold them in their minds, they have this fear that you might inject them, that is also stress. Remember that pigs are intelligent animal and they do adopt.
One option you could do is use a shorter needle if you want to inject subcutaneously. Give them feeds then while eating inject to the neck