I'm sure the APA would tell you that they aren't "getting around" McCaskill-Bond, they're just applying it as it's supposed to be applied. Whether that is actually the case will probably be up to a judge to determine, but it would seem that the APA has the upper hand with the way the MOU was written.
But as far as the APA just intentionally screwing over the Airways guys, they would be wise not to do that. Once they represent Airways pilots, they have a duty of fair representation (DFR) to those pilots, which prohibits them from acting in a way that is "discriminatory, arbitrary, or in bad faith." In other words, they would need to have a rational basis for whatever way that they merge. Just screwing over one group of pilots that they represent in favor of another group would be a clear DFR violation.