Abortions were prohibited in military hospitals in the 1990's, and their re-institution would come with the caveat that women would have to pay for the procedures themselves. In other words: no government funding. Still, it's going to cause consternation among anti-abortion groups.
Recall that Secretary Robert Gates supports the DADT repeal, but only after the military has had time to implement the changes over a period of time -- giving the institution time to adjust. The Congressional mandate would throw all of that out of the window.