Blender 2.58a is the second stable 2.5x release from the Blender Foundation.
Source:
http://www.blender.org/download/get-blender/
I haven’t had any problems with it.
You can do your modeling in both versions, not much there has changed but a few hotkeys. Yet the programming side has.
Since you’re focusing on programming currently, it may be in your interest to start that with 2.5 instead of do programming now in 2.49 and have to convert it to 2.5 when you get your model done or are ready to put it in.