...against a fellow Starfleet ship? That very point was addressed by Khan and Joachim moments before, which the screenwriters anticipated would be a question. If you raise shields against a fellow vessel simply because communications cannot be established, then there's something not quite right about Starfleet.TWOK
I don't even have to spell this one out. Raise the goram shields.
Except Saavik seems to be trying to warn Kirk about a regulation that tells them to do just that.
SAAVIK: Sir, may I quote General Order Twelve, 'On the approach of any vessel, when communications have not been established...
SPOCK: Lieutenant, the Admiral is well aware of the Regulations.
SAAVIK: Aye sir.
I'm sure Starfleet had seen occasions where their vessels had become compromised and boarded by enemy forces before (heck, we saw it happen to the Enterprise a few times in TOS!), so the regulation is clearly there for a reason. Somewhere in Starfleet's past, a precedent was set that made General Order Twelve necessary. The whole point of the scene is to make Kirk look like a jackass for not following regulations and raising the damn shields, no matter how much he'd like to believe a 'friendly' hasn't been taken over by unknown forces. Nobody's asking him to open fire on the Reliant, but General Order 12 is clearly there for a reason. Kirk ignored it, and paid a price by not raising the shields as a precautionary measure only.
But this is the thing: by rights, 'coil emissions' or no, 'Chekov' or no, General Order 12 exists for a reason, and Saavik quotes it for a reason. Kirk's folly is in completely ignoring the advice he's being given. What happens next (including the many deaths of which Preston was only one of them) is wholely on his shoulders, because he decided not to follow General Order 12 and raise the shields at the first sign of trouble.