You are comparing apples to oranges. Westboro is certainly NOT a member of the SBC, and does not have any military chaplains (since they thank God when soliders die). So who is the arbitrator in the SBC that determines when a pastor is "going against scripture"?
>> Now blatantly go against scripture and you might be asked to leave. <<
Again, by WHO? A random member of SBC who thinks the pastor is going against scripture? How would that work? Random Baptist Christian in the military: I really think you should leave the SBC because you support gay marriage. Chaplin: No.
>> In the end the local congregation. <<
As has been previously pointed out on this thread, military chaplins are not under a local congregation.
According to Wiki: Military chaplains must be endorsed by a religious organization in order to serve on active duty
A military chaplain must be endorsed by a religious organization in order to serve on active duty. In the contemporary U.S. military, endorsement is a complex area and many different paths are available. This religious endorsement must be maintained throughout the chaplain's military service and can be withdrawn at any time for religious or disciplinary reasons by the religious body with which the chaplain is affiliated,[4][5] though provisions exist for exceptional cases.[6][7] A military chaplain's rank is based on years of service and promotion selection from the appropriate peer group. Each is identified in uniform both by rank and religious affiliation insignia that indicate as well the branch of service.
This is how it works: each SBC church sends what they call “messengers” to the SBC Convention each year. Those are people who have volunteered, or been asked to go to represent their church at the convention. Any messenger can bring up a problem within the SBC church body: i.e. other churches which are preaching non-truths (and please keep in mind, these would have to be a big departure from Scripture — i.e. gay marriage is fine and dandy with God and that body does not condemn it and even supports it; the pastor is gay or is having an affair with a member of the church (although if the congregation is doing its duty that issue has probably already been dealt with locally), etc.... The church can be voted out of the SBC: messengers sent from that church would not be seated, funds sent from that church would not be accepted. In essence, the church would be no longer welcome within the SBC. As another poster has pointed out here, this does not happen often — but it does happen when a church goes heretical in its preaching/practices. (I’m thinking we’ve had this convo before, no? Something regarding Boy Scouts?)