I'm inclined to say no, especially if what MLB is interested in is increasing diversity on the diamond, which appears to be one of their concerns. Most college baseball programs tend to be whiter than a fifty-pound bag of rice to start with, and having MLB pony up for some additional baseball scholarships isn't gong to make that much of a difference. If MLB really wants to change the way college ball operates, they need to quit being a bunch of damn cheapskates and spend the money necessary to get the NCAA out of the business of baseball, period. Players who are going to college should be allowed to concentrate on school during the school year and then go out in the summer and pay for actual money on teams associated with the colleges. Hell, I have no problem with colleges running minor league teams as a sideline, for that matter. This nonsensical ideal of the "scholar-athlete" needs to be disposed of, though, because if it's implemented with MLB cash, you're going to have kids used and abused by colleges for the ultimate benefit of the MLB the same way they are in basketball and football.
If MLB is really concerned that black kids aren't getting into baseball as much as Latino or white kids, maybe they ought to consider spending some of the money they put into the Dominican and Venezuelan baseball academies on similar schools in their home towns. There are a lot of kids who don't have the physical tools to play basketball or football, but they could be great baseball players if they got the chance - and if nothing else, they'd get an actual education, which is more than you can say about the public schools in a lot of major league cities.
Just say no to the NCAA, Commissioner. Drive them out of the baseball business and replace them with minor league teams operated by the colleges and at least partially funded by MLB. In the long run, it would be the best way to achieve the goals you say you're after.