They made the switch to be competitive, which is more important than keeping the M3 in the series.
The M3 has been pushed to the limit and in recent years, could not keep up in the straights (due to regulations and whatnot).
http://www.bimmer **********/content.php?2585-ALMS-2012-BMW-blames-new-technical-regulations-for-the-4th-and-8th-place-finish-at-the-2012-Mosport-Grand-Prix