That's conflating two things, yes. The pick, and then what happened subsequently in a different roster move. It's one thing to draft a player that turned out to be awful. It's another thing to draft a player who turned out to be great, but you made a SEPARATE decision after a year or two to trade him and he spent the rest of his career with another franchise.
In the first case, you made a bad draft pick. In the second case, you made a good draft pick and then made a bad (depending on the return) trade of what was a good draft pick.
Like you said...this really is pretty simple. Favre was a really good draft pick for the Falcons. They then made a really bad trade of a really good draft pick.
JG was a good solid draft pick for the Patriots, even though he took A DIFFERENT TEAM to the Super Bowl.