There's enough differences that I think they'll just bite the bullet and change them slightly. The most noticeable difference, of course, is that in the anime, the episodes immediately following the events in Lior are flashbacks to before and just after Ed's appointment as a National Alchemist, whereas in the manga they continue along a linear chronology.
I'm sure most people would be more excited about the latter episodes anyway. It's around the time of (SPOILER)Maes Hughes's death that the two continuities clearly diverge. The manga's explanation of things tend to be significantly more in depth. I'd especially like to see Roy and Riza's history expounded upon. There are enough drastic differences even just shortly after the two diverge that nobody would have to worry too much about rehash.