This is just an opinion, but I think medical schools will see the program as part of whatever total picture you show them. Consider a few things...
1. How much can taking a course online change the material? If you remove a possible laboratory component from consideration, what is different about the brand of histology online students are getting? If you call a course medical neuroscience, you damn well better be presenting medical neuroscience.
2. Consider modern lecture courses, they are often taught with Power Point presentations, online study aids, text books, movies and sound bytes. Consider how many medical schools podcast their lectures. Taking these courses online may prepare you for medical school in a way that students taking the same courses in a traditional setting are not getting.
3. Do you have a legitimate, unique or interesting reason for enrolling in the online program? If so, it is well documented (both in these forums and other places) that medical schools love diversity in their classes. Taking these courses online allows you to deal with whatever issue prevents you from attending traditional courses, while allowing you to continue your education at an advanced level. How many other applicants will be able to claim anything remotely close to that? The usual scenario involves taking a year off between undergrad and med school to deal with an issue or to strengthen your academics. Doing both at the same time is unique.
4. Don't forget that a great deal of self motivation and determination will be required to get these classes done. There will be no one to hold your hand, to remind you of assignments due, to make you watch the lectures or to do the reading. While this is usually the case in most college courses, it is even more true with online courses. You will determine how much work you do, how much you get out of it and how well you do.
5. From what I gather, this is the inaugural year for the 100% online mater's. That means you have the opportunity to set the standard as to how schools view the program.
This may not be the traditional method of doing things, but as Jvillegator said in his post "at the end of the day it is a program through a US allopathic medical school, so it can't be completely written off".