I don't know about calling him a good GM, if we're going to consider Jerry West the benchmark for executives doing their job properly and on-court success in measuring a GM's performance then calling Isiah Thomas a good GM is being generous. However, the suggestion that he wasn't all that bad and all the doom and gloom is an overreaction is an interesting one when you look at his tenure from the perspective of that article. I think this paragraphs gets at the heart of the matter:
The impact of Isiah’s GM mistakes has always been grossly over-rated [5], and effect of his terrible coaching (and Larry Brown’s) vastly under-rated [6]. Isiah’s biggest GM errors were ones of chemistry (see Steve Francis and Randolph trades). But GM's who move into abandoned buildings can be forgiven for collecting furniture at garage sales that might not match. Talent can always be swapped for other talent to improve chemistry. Rarely is the reverse true. While Isiah did a lot of the dirty work, few in media acknowledged his toxic working conditions [7].
He certainly managed to acquire some talented players through trades and the draft and his Knicks teams didn't always look too bad on paper; with the way the East has been weak at the lower seeds during the past five years making the Playoffs has not been a completely unreasonable goal, and indeed they qualified for the postseason in 2004, so I'd suggest Isiah's teams did have the potential for some modest success. As we all know though, the great paper teams aren't necessarily cohesive units on the court and all manner of personal and professional issues can combine to derail the season.
Then again, the opposite strategy isn't necessarily any better. The article brought up John Paxson's mistakes which is an interesting comparison because Paxson's strategy has tended to be the direct opposite of Isiah's, bringing in or getting rid of players based on perceived character "issues", at the expense of losing a good player. It's arguably had a little more success to date but not by enough to suggest it's definitely a better approach and now the Bulls find themselves in a similar position, so the point that the blunders of other GMs are overlooked or underrated compared to Isiah's mistakes is a good one.