I agree with much, though not all, that famous African-American sportswriter Howard Bryant says here. A few points:
There is good reason to recognize the top Negro Leagues as major league, given 1) many of the players were clearly good enough to play in MLB and the best ones were good enough to be Hall of Famers (some have in fact been inducted). Several were likely among the top players of all time (Satchel Paige, Josh GIbson, Oscar Charleston, etc.). It is also true that MLB previously recognized several non-MLB white leagues from the late 19th and early 20th century as major league. The standard of play in several of those leagues was no better than the Negro Leagues, and quite likely worse.
But, for reasons, Bryant notes, integrating the stats from the Negro Leagues with those of MLB is more problematic. I would add that it's actually hard to gauge whether the quality of MLB and Negro League play really was on the same plane, overall. One difficulty is that NL leagues necessarily drew from a much smaller population than MLB (about 1/10 to 1/8 the size). Even if you assume that the black population had had a substantially larger per capita pool of topnotch baseball players than the white population, the talent pool for MLB was still much larger. As a result, stats compiled in NL were generally compiled against weaker opposition than in MLB - NOT because black players were somehow inherently worse than white players, but because of the size of the two talent pools. A league that, e.g., could only draw on players from California, would suffer the same problem relative to one that could draw on the the entire rest of the nation.
On the other hand, it is also true that several of the white leagues whose stats were integrated by MLB have similar talent pool issues. Perhaps that integration (decided on in 1969) was a mistake. The whole issue is a knotty problem. But my tentative judgment is that MLB should recognize these leagues as major league, reiterate its recognition of the injustice of segregation, but keep the stats separate. We should also keep on inducting Negro League players into the Hall of Fame, in cases where the best available analysis suggests they are worthy (a good many have already been inducted, but some good candidates may have been missed).
As Bryant suggests, the whole issue is an example of how it's often not possible to truly undo a major injustice decades after the fact. We can't simply go back in time and give those players the opportunities they deserved. Ditto for many other victims of racial segregation, of course.
It is also worth noting that this is NOT the only case where players were kept out of the top professional leagues in their sport, because of morally invidious reasons. Consider the following examples, which have not yet gotten as much attention as they deserve:
Cuban players from the communist era could not play in MLB unless they defected (which meant risking one's life and freedom and retaliation against the player's family in Cuba). There is little doubt that a number of Cuban players who were barred from leaving were good enough to play in MLB, and a few good enough to be Hall of Famers. Should MLB integrate the stats of the Cuban national league and/or induct appropriate Cuban stars into the Hall of Fame? I favor the latter, but not the former.
Until the 1990s, it was nearly impossible for Japanese players who played in the Japanese domestic major league to move to MLB (though some Americans played in the Japanese leagues). Some Japanese players of that era were clearly of major league quality, and a few good enough to be Hall of Famers. Sadaharu Oh hit 868 HR in the Japanese league, and would be the all-time HR leader if the stats were integrated with MLB's. I highly doubt Oh would have hit that many in MLB. But he would likely have been an HOF-level player. Here too, I don't favor integration of stats. But Oh and others should be made eligible for the HOF, and inducted after appropriate consideration.
Until the late 1980s, hockey players from communist nations could not play in the NHL unless they defected. It's very clear that the top Soviet and Czech/Slovak players of that era were good enough to play in the NHL. Slovak player Peter Statsny, the best of the defectors, was one of the 5-6 best NHL players of the 1980s. The NHL has dealt with this issue by allowing induction of Iron Curtain-era eastern European players into the Hockey Hall of Fame. But they have NOT integrated stats from the Soviet and Czech leagues of that era (and for good reason).
What is true of hockey is also true of basketball. The best Eastern European players could not play in the NBA until the Iron Curtain fell. They were a less significant proportion of all the best players in the world than in hockey. But the best were still good enough to play in the NBA, and a very few (e.g. - Arvidas Sabonis) were good enough to be Hall of Famers. A few have in fact been inducted into the HOF, based primarily on their achievements in European and international play (Sabonis is the best known).
The above is not an exhaustive list, and I'm sure there are similar issues in other sports I am less familiar with. My tentative judgment is that we should find ways to recognize the achievements of players excluded by unjust rules, include them in various halls of fame (where appropriate), but be wary of integrating stats between leagues with differing rules and conditions and sometimes widely divergent standards of quality. We can't fully undo the evils of Jim Crow and the Iron Curtain, and we should not pretend that we can. On the other hand, we should honor achievement wherever we find it, to the extent feasible.