But they basically are SHIELD. They're guarding SHIELD stuff, they are SHIELD-adjacent. They're not bad guys, they were people put there by an organisation that clearly has ties to SHIELD and is opposing the same people as them. It is like US troops killing English troops in Iraq or Afghanistan. They're not US troops, but it is still a bad idea, especially if they want us to cheer on these guys. I wouldn't mind a good antihero, but they're supposed to be heroes, not antiheroes.
Within the context of what we saw, we have no way of judging the goodness or badness of those two guards. Though I will say that with Coulson explaining several times their situation:
"How was the drive from Istanbul?"
"This is Agent Coulson with SHIELD. We don't know the counter, but we have a team member in dire need of assistance. We know she can be treated here. Open the doors. Maybe we can work something out. Do you copy?"
"How was the drive from Istanbul?"
"We're looking for medical assistance. A person's life is at stake. Will you help us?"
"How was the drive from Istanbul?"
"We've come for medical assistance. But if you continue firing on us we will be forced to defend ourselv..."
I wouldn't necessarily say the guys were "good", if they were to ignore such a plea. And if they really are associated with SHIELD (which is doubtful, as Fitz couldn't find anything in the SHIELD database about the protocol the guards used to test them), then their should've been another way to verify that Coulson and his team were legit agents.
Ultimately, Coulson knew that the cure was there, and did what he had to do to obtain it. He'd prefer to do it peacefully, but those guards tied his hands. His other alternative would be to let Skye die, which while this would be acceptable to some of you guys, would be unacceptable to Coulson.
Also, to refresh your memory, this is all the info they had on the "Guest House" before they went there:
Coulson:"The guest house is not a SHIELD facility. We don't know who or what's in there. Be prepared for potential resistance."
Agent Garrett: "No contact from inside?"
May: "I've tried every known channel. No response."
Agent Ward: "Place could be abandoned."
Coulson: "Let's hope not. We need the people inside to work on Skye."
There's more, but this dialogue shows that all their info indicated that this was NOT a SHIELD facility. They thought there could potentially be hostiles, which would mean they might have to shoot to kill. They ultimately did try to be diplomatic, several times at that.