The argument that none of us would have thought to take any other weapons into that situation is patently ridiculous. Frankly, if I were going up against an unknown number of assailants with super strength I would have been packing a small arsenal. I always wonder why heroes and law enforcement in comic books/CBMs don't just cap some of these low-level villains in the head and be done with it because that's sure as hell what I would do. There is no reason on Earth why someone like Joker shouldn't have had his grey matter splattered across a sidewalk long ago. That's one of the reasons I love MCU Tony Stark and Steve Rogers so much. When given the chance they will kill the bad guys without even blinking 'cause that's how they roll.
It turned out these super soldiers weren't really bad guys, they were slaves controlled by an eye piece. I don't want my TV heroes to be shoot first ask questions later types, resulting in them killing folk they should be helping. Mike and Akela got second chances, why not these soldiers?
Coulson's team are investigators who want to find out what's going on, not soldiers who will kill any potential threat. Personally, I prefer that.