there was a post not too long ago where someone tried put OEM M6 rims on his E39, they didn't quite fit, so he just torqued them down and forced them on. Needless to say, he had a lot of vibration problems.
It is possible to bore them out, but I'm not sure what the cost would be.
I think the aftermarket ones by Miro look really good, and you can get them in black with a red stripe ala "time attack edition". I would just go aftermarket if you are looking for E60 M6 or M5 wheels for your E39.