We haven't upgraded our BES servers (which are currently on Server 2008 R2) to SP1 yet. But I suspect, there could be some problems with the BAS service, as some kernel security updates last and early this year caused some problems:
KB23927-BlackBerry Administration Services continually stops and restarts, after an operating system hotfix is applied
I am pretty sure those security fixes are included in SP1, so it might break BAS and you can't uninstall them separately. So I would hold off with SP1 until it is officially listed in the compatibility matrix for BES:
BlackBerry - BlackBerry Enterprise Server Compatibility
My guess is that BES 5.0.3 will be compatible. So we are waiting as we have no pressing need to upgrade our 2008 R2 servers to SP1.