My gut feeling is that B6 will be tapped by someone. It's almost inevitable. No airline can get enough of the New York market. B6 has a pretty good amount.
Depending on precedents set by other mergers/acquisitions, you still might be better off at B6. I'm not a lawyer, but if B6 had the supposed protections of a union, I would say hands down, don't wait another second and get to class at B6. I just don't know how much laws like McCaskill/Bond could actually protect a pilot group without any other legal protections. Protections such as scope, time frames for integration, language that any acquiring/merging body would have to abide by legally. This is language that has to be carefully crafted. And in most cases, it is most commonly acquired through a CBA.
Atlas is a fine cargo carrier. I don't foresee them going anywhere anytime soon. Perhaps they too could be part of the consolidation game via UPS or FDX, who knows. I am aware of their integration of Polar.