It was not a public rehearsal.
Just no one bothered to stop Blackout from entering. or, if he did, he didn't succeed.

Coulson tried to talk his way in the Safehouse and explained exactly why he needed help.
They just refuses to answer and started shooting.

My idea is she selected the coordinates of the place where the disk will decrypt.
She must go there, they must know where she will be and wait her there.

She saw blood on Ward first to find Koenig. Ward go away and do not allow her to tend his "bleeding wound". The blood, also, match with the position of Koenig: he dropped from above on Ward head.

Knowing SHIELD, they could have a secret base located under a secret base.

Bond girls are one for movie and always changing and you can see any Bond movie as a single shot.
Writers have definitive limits about what they can do with the characters and the limit is Marvel.
If you have an Agent 13, she will be Captain America love interest (in the comics she got pregnant with him, also).
They…

Apart Coulson, are they all HYDRA?

They will pardon Fury when he deliver them from HYDRA.
And with the infiltrations, they could just blame HYDRA.

The first beams were from afar.
Reason enough the Dark blasts were not strong enough to kill.
The bad guy exert himself being hit and attacking back.

Skye is getting better and better as an Agent of SHIELD.
In "The Magical Place" she went off grid, found Coulson, interrogated a man, managed a confrontation and defeated the SHIELD bracelet. She also landed a KO punch on Flowers. And she was not shoot twices.

The blood on Ward was not his blood and he left abruptly when Skye discovered it.
This is the reason Skye jump from "Koenig dead" "Ward is HYDRA".

Maybe, just maybe, he had not tape and just a penny.

They are building her part for the following movies, like they did with Black Widow.
You can not just put Agent 13 (the love interest of Cap America) in without any base. Just notice how Natasha continuously ask Cap about his sentimental life during CA:TWS.

Interesting enough, I saw the scene on "Seeds" in front of the agents memorial at the end of the episode. They show Ward when Coulson talk about "evil, betrayal, etc."

Reina is here to change the world.
She never expressely said she shared HYDRA plans.

Very intelligent people can be very naive and very cunning at the same time.
Everyone have some blind spot.

I would say this is not in the interest of HYDRA,
Master of Evil is the creation of Baron Zemo.
There are, securely, more groups supported, competing, with HYDRA and with the same end goal (world domination).

I would say he is just very protective; they are very protective each for the other. Obviously there is some story behind it. SOmething off the records of the SHIELD.

True.
Lovely the line of Captain America:
"Before we start, anyone want out"?

Whedon is doing Angel with Ward.