Logically thinking about how SHIELD operates, I'm pretty sure this happened after the fact. Often, TV shows and movies don't necessarily show the more routine portions of investigations. The "clean-up" is usually implied.
I'm pretty sure the gauntlet Coulson dropped in the form of "fly over a SHIELD-allied country and we'll shoot you out of the sky" was just that. As the show has established, there are certain nations that SHIELD has no jurisdiction over. I'm pretty sure Quinn's public/known assets in SHIELD-allied countries have already been seized and/or frozen. However, for someone who is as adept at making the shadiest of deals for black market tech, I'm sure he's quite capable of moving money around quite easily. I mean, even in real life, cartel kingpins and the like get up to quite a bit of nonsense despite being quite publicly branded as enemies of (various) state(s).
I actually agree with SHIELD's decision on this. Also, I think you're thinking about the Fridge, which is the containment unit that Coulson used to house the Gravitonium blob. The Sandbox is a research facility... it's where they dropped off the Chitauri helmet in the FZZT episode. Were I a SHIELD higher-up, I'm pretty sure I would take a want-and-see approach before continuing to train Donnie, considering his dangerous and quite criminal actions. Yea, the same can be said of the Item 47 goofballs (and possibly Skye), but those were Sitwell's and Coulson's respective judgement calls, I guess.