...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.