It really depends on the attitudes of the faculty. At Greenville Presbyterian, there are a bunch of Baptists. Several of the faculty were once Baptist. We have Reformed Baptist pastors preach in our chapel sometimes, because there are a lot of good ones around. At the same time, none of the professors are hesitant to tell us what they think on the issues.
If the faculty respects Reformed Baptists, then there shouldn't be a problem. It's not that bad to sit in class and hear someone say something with which you disagree. It may even strengthen your convictions (although I became Presbyterian since attending GPTS, oops). Now, if that school is always talking about how Baptists aren't really Reformed, and they can't be covenant theologians, and their form of Church government is against the essence of the church... I wouldn't go there for ministry training.