I wouldn't let the A&M Chancellor and his administrative blunder dissuade you from applying. I don't see this working out well as I have written about elsewhere. But perhaps I might be able to ease some concern.
When I was a student and was in meetings with HSC and COP administration the idea of a second campus was talked about and rumored but was not official. As I understand it, according to the law that established the COP in Kingsville, the COP promised ~120 graduates per year. Unfortunately the building that was started by TAMUK and finished by the HSC was too small to accommodate that many students. So realizing the legal mandate it is necessary to build or expand to fulfill the promised number of pharmacists. There is also talk of further expansion on the TAMUK campus (at least while I was there). The expansion of a second campus to Bryan/CS is two fold: 1. to increase enrollment (the legal requirement) and 2. to bring everything under the Main A&M administrative umbrella (the Chancellor's ploy to get more "research" $$).
The main A&M administration may not (hopefully) be involved in the day-to-day operations of the school. There is still local administration (Dean Reddy, Dr. Peterson, Robertson, etc.) that are more hands-on and knowledgeable about the goings-on in Kingsville. The school is heavy on technology and broadcasting lectures due to faculty involvement with rotation sites, so that probably wouldn't change.
As a plus, and this is just may opinion, I think a campus in Bryan/CS opens more opportunity for rotation sites, especially Veterinary Pharmacy as A&M has one of the best Veterinary schools in the country.
What all this boils down to is, I would not base your decision to go the A&M based on the administration that's 4-6 hours away. Its the faculty, COP administration, your feel for the COP, and personal choice that matters. Living close by I would see about a tour or visit the building if you haven't already. In the end it's up to you.