I crossed ACS off of organizations I support because of this....and I was about to organize another relay team. What concerns me most is how does such blatant discrimination affect other aspects of their charity work. And, yes, the way ACS has handled this has only made the issue progressively worse.
Komen and Livestrong are both reputable alternatives for anyone looking for a secular organization to support.
In my line of work, it's difficult to understand how organizations who depend on support would be stupid enough to act this way. But I've seen the ACS go from great organization to bloated, unwieldy, and obsolete in its performance. Too little of the money donated gets to where it needs to go with them. This further exemplifies how badly it's being run.
I give to, and volunteer with other groups, such as the Leukemia and Lymphoma Society, the Multiple Myeloma Research Foundation, and smaller non-profits, who get the funding to the people who need it most urgently, rather than to their executives.