This is what was bothered me. I had been assuming that a big part of what was bothering Coulson about his discovery was the ethical situation. If that thing is still actively producing whatever they need from it, there's a real chance that it was being kept alive in that tank for that purpose, and that's fucked up. But then he clears the air with Skye and it's all about giving her a drug that he thinks is alien.
Not sure why that made so much of a difference if that's all it was because he didn't know anything about the drug in the first place, which should have given him the same concerns he had about it being alien. In either case, his issue is that he doesn't know what it is or what the side effects could be.
Then there's the issue of killing those guards. It really didn't help that situation when the very next episode went right back to the knock-out guns from earlier in the series.
