At first glance, the second one might appear to be a better mark. However, if you don't know what it stands for, or that the top part of it is an M, the graphic is just an ordinary arrow. It doesn't accomplish the primary goal of the design.
Good logos don't beat you over the head with what they mean. The original version is pretty amateur in that respect IMO, it is almost the first thing anybody would come up with.
Having a bit of delight and 'aha!' in a logo is a good thing.
http://dribbble.com/shots/423934-This-Means-Markdown
Another nice one:
http://dribbble.com/shots/424152-Markdown