Okay, I'll start with an example. (Something I experimented with.)

I stroll on over to Helios One to set the two outside terminals. East...set. West... vicious dogs. I beat 'em down with a bat, turn to check the radar, all former "white marks" are now red. I'm approached by hostile NCR-- I'm assuming it's because of the dogs? Boone and ED-E open up, clearing the threat. Soon after I'm notified that I'm now "Vilified" by the NCR without firing a shot. Boone then tells me he'd rather die that further betray the people he served with.

Now that being said...

I understand that you take full responsibility for your followers' actions. But them being mad at you for them killing who they hold dear... WTF?

I think the dogs are bugged, they are supposed to be BoS dogs (at least I have heard this here multiple times and everything on the Internet is absolutely true. But, if they are BoS, why didn't the NCR just shoot them?), but they screw up NCR rep. I kind of think maybe they are an NCR defense item and we just never hear about it before we start the quest. I don't recall being warned about hostile dogs. Maybe, since it was the first real time I could REALLY mess with the NCR they give you a little test to make sure your serious about helping them.

The nice thing is they are places so it's super duper easy to get by them and access the terminal with a Stealth Boy. I originally got too close with Boone and he took off into the cage and next thing I know I'm getting shot at.

I wish we had a command to tell the companions not to shoot unless they receive damage.

I just ran there, hacked teh computer and ran out closing the gate behind me. Those dogs can't punch through combat armor at all.

Oh I had trouble with those dogs at Helios One. Ended up leaving my companions in the building and using a stealthboy to get in and activate the terminal then legging it. Fortunately once you've shut the gate on them they can't get out and the sandbags prevent them from spotting you.

The dogs at HELIOS One never messed up my rep. I just assumed they went feral and the troopers are just lazy, like they are about everything else.

I think the dogs are bugged as well. if u target one in vats it says'NCR trooper dog". I had the same thing happen to me today, if u/ or companion harm the dogs then the other ncr troops will be hostile towards your party. i had to use a stealth boy as well to get thru that part of the quest. with so many bugs/glitches around the helios 1 quests i am wondering if i should wait till the next patch to finish it.