The ending of No Hero didn't make sense at first. The governments of the world had to know that destroying Front Line would completely screw things up and lead to economic collapse and leave the world on the brink of world war since they've been planning their scheme for decades and knew full well just how well connected Front Line was. Then I realized: they made the same choice their hitman Josh did at the very end. They too are willing to follow a course of action that would likely result in chaos and death if it means they can "get to choose something" again. - M84
Alternatively, they were planning to take Masterson alive so they could learn about his FX7 and keep the world stable. They had intel indicating he was effectively immortal/invincible, so even if Joshua disobeyed orders or got too rough, they didn't have to worry about him getting killed. However, they hadn't counted on Joshua finding a creative way to get rid of him.
In-universe: The two government agents speculate on what it'll be liked trying to deal with Joshua now that he's been enhanced by FX7. They decide not to think about it too much for the sake of their sanity. Luckily for them Joshua is content to off himself after dealing with Carrick.