I am sure that some Congressmen will have to make it an issue if they have a University that is somehow "left out". I remember the reactions of Harkin and Culver a little over one year ago when ISU was potentially frozen out. You have to be some sort of conspiracy theorist to believe that all this is planned and that is how Congress would pursue this.
All this realignment started off with the Big Ten wanting to add one team and suggesting it might as many as five. The PAC 12 simultaneously began expansion and added two after entertaining the idea of six. Now the Big Ten is not actively seeking new members and two conferences; ACC and SEC, are in expansion. But just a total of three team; A&M, Pitt, and Syracuse. This hardly warrants Congressional inquiry.
The two affected conferences still exist, but seem unable to be able to resolve their problems. That is something Congress needs to realize and avoid involvement.