Exactly, the only reason people are considering them to be "good" now is because they're associated with Konoha, who have always been "good" to the viewer/reader.

The trio is still the same as before, just following orders like before (with the possible exception of Gaara who hasn't killed Lee yet so he may have changed somewhat for the better).

In the same way, the only reason they were considered evil before was because they were up against our heroes, Konoha. You have to remember that this wasn't their own decision, they were following orders so they were never truly evil by their own devices (Gaara is a different story for obvious reasons).