It's a simple check:
On initiating dialogue with normal NPC
If Monster in party = very yes
Then NPC reaction = "AHHHHHHHHHHHHHHHHH!!!!!!
You don't need to modify every NPC in the game, just have it so that the game checks before you initiate dialogue what's going on.
On doors for large creatures you just give it a value where it accepts a large creature or not, and, if that value is false, the game says you cannot enter since a member of your party cannot fit.
It doesn't have to be a horrible amount of programming if you have an efficient system to begin with.
I take it you never did scripting for BG or NWN, right?
If you did, you'd know better.
On another point is that the only reaction there will be?
(unimportant) NPC fleeing? Surely that makes the companion tottaly balanced!
Large creture cannot enter? How do you do quests taking palce indoors then? You'd have to switch companions constatnly. And I'm willing to bet that would case a lot of player rage.
No, I didn't do scripting for BG or NWN, but it is possible to make the effects occur in a simple manner without having to edit every NPC's files. If NPCs turn and watch you, getting ready for you to talk to them, then there's clearly somewhere you could shove in a party check before dialogue actually initiates. Or you just have it be a line of sight thing with most NPCs, and only have disciplined/important NPCs be willing to stand their ground as the giant walks down the street.
And really, that should likely be the response for any "normal" NPC, with guards likely having a different response, etc. Before initiating the dialogue, check if the NPC is unique or just your average peasant, if they're unique, they likely have their own response to the fact the monster is in the party, be that turning hostile, having a moment where they stutter in fear, or whatever you have.
And large creatures not fitting through a door could be helped with a minimize spell (something useful for getting into tiny places for cool loot, and also makes you harder to hit and you more likely to hit) They'd obviously lose some of their awesomeness for a while, but you'd get to at least have them there... and if it wasn't worth your time to get or prepare said minimize spell then you can just tell them to wait for you until you get back. Or you can decide it's not worth your time to try and keep them and just let them go for another, less powerful/interesting NPC. The point is you're making the trade off - if they're worth the effort, you gain the benefit, but if they're not to you then it's at your discretion to do away with them in whatever manner your PC would see fit.