If I remember secondhand stories right, the Harley course is the MSF course, with Blasts instead of assorted 250s, and with a dollop of Harley marketing lumped in. So for the safety aspect, it's the same course. The Blast isn't the best of bikes (the 2010 was the best by far) but it's plenty mild enough to learn on. Some of the students complain about it; IIRC the clutch pull being stiffer than most learners was the most common. A regular MSF course -may- have a variety of bikes to train on, i.e. Rebel cruisers, a mild dirt bike, etc, which is especially nice for shorter or taller students, but this varies by location. The quality and experience of the instructors is also going to vary by location (for Harley and vanilla MSF.)
I think it's a matter of price, scheduling and location, if the Harley class is closer, cheaper, and sooner than the MSF, sure, otherwise pass.