The thing is... it's not
just about killing the guards. If the Guest House facility was deemed by SHIELD to be a threat, and it was a mission objective to eliminate said threat, then Coulson and team would have every justification to do exactly what they did. But what mission were they on? Save Skye? Nope, not a mission. I'm sure agents are killed in action all the time. No orders (that we know of) came from higher up.
From everything Coulson knew up to this point, it's stupid of him to assume that the Guest House was a threat rather than an asset (on the books or not), and ultimately be responsible for its destruction. Again, I understand that it's not a SHIELD facility, and that it might, in all probability, turn out to be the property of some nefarious organization... HYDRA mostly. However, based on what Coulson knew at the time, that assumption is completely unjustified, and thus, his course of action, ridiculous.
And if Coulson knows something that hasn't been revealed on the show, i.e. the ol' unreliable narrator trick, well, then that's bad writing in it's own right.
Logically, Fury would be livid at this situation. He'd pull a Jules and come after Coulson with "great vengeance and furious anger".

However, I'm sure we'll basically be back to status quo in the next few episodes. See, that's my main problem with the show... it's internal logic is contradictory at it's worst, and inconsistent quite often. The show-runners ought to know better.
Look, I loved everything about the episode in isolation. Like I said, the (probable) Kree? Arrrrgggghhh!!! Loved that. Trip and (especially) Garrett? Awesome! New blood! Paxon, at that! Yay! Fitz-Simmons holographically querying SHIELD databases? Nice. Quinn mugging for the team and being "overconfident evil guy" even though he came close to having his tongue ripped out? Hell, yea! Love me some over-the-top villains. The airborne docking sequence? Awesome.
Unfortunately, the overall plot did not rationally bind together all those independently cool elements.