Why are they giving wish fulfillment to a dead villain? LOL
Fan service gone wrong.
They most likely realized having a narrative that glaring had to stop at some point.
When your protagonists say over and over they are the good guys, while they are clearly doing some evil shit isn't the best thing to have. Most of the team are murderers, they constantly threaten and torture people, they create a lot of the threats they try to stop.
It was a long time coming they start to face consequences for their actions, even if it's just at a personal level of "well shit I didn't handle that very well and caused more trouble than I've fixed".
Coulson is the only reason Hive was a thing, knowing he went too far he toned it down for a moment but then resumed doing whatever the fuck he wanted again, just like he did after the second shield.
This whole arc has been about fucking with the team emotions and perception of reality. Having Coulson knowing that Ward might not have killed everyone he did (including Rosalind) if he just left Ward rot in a cell instead of trying to "invent new ways to ruin his life", is plenty to fuck him up even more.
Him not being a shield agent isn't close to anything the others are going through.