I'm a little unclear on the process but I'll go through what controls I'd put in place and why.
The purpose is to keep out pathogens, particularly Listeria, heaven knows, people probably didn't think about it much before Bluebell but it is a hazard that it could increase to dangerous levels in your mixes and then survive freezing so you want to keep your production area as clean as possible.
Personally I would put a hatch in the wall specifically for transferring the packaging to avoid water splashes etc in the changing room.
There are a few ways to do this. Firstly, keep out the cardboard. So the first control could be to have someone pulling the bag of primary packaging out of the card box while another member of staff holds onto the box on the low risk side. Not very practical. Why not just handle the box from low risk? Well then you have transfer from that low risk person. You could "tip" the box out into high care but again this could transfer some contamination. It's all pretty theoretical though as the boxes should be dry. That said I have found Listeria in card before (long, long story.)
The next step up from this is to have a double layer of protection so within the card box the primary packaging is double bagged, the outer bag is removed at entry to your high care area.
Lastly as you say you could spray the bag with disinfectant.
Which do I prefer? Probably double bagging because it's easy to do but the disinfectant will probably work best as even if there is some transfer from the outer, it will be killed. It really depends on what ingredients / hazards you have on your low risk side as to how much risk there is, that said, Listeria is ubiquitous and it only takes one breach to be an issue. Whatever you do, validate the process and do verification swabs from time to time (both Listeria and TVC).
Ultimately it's a good question. If a process isn't happening you need to either change processes so it does happen or enforce it.