I am totally confused on this one!
I have a colt preban lower, and I'm in the process of purchasing an Armalite postban upper.

Well I called Armalite to see what I could do to change the muzzle brake out to put a flash hider on it.  Armalite said a post ban upper could only be attached to post ban lower.  AND you could not legally make a post ban upper to preban(going on preban lower or not).  BUT, I could purchase a preban barrel from Armalite and put it on the postban upper receiver and preban lower.

The gunsmith around here won't even discuss removing the muzzle brake.  so what do I do?

I think maybe he misunderstood you.  I would hope those guys are not that mistaken about the law.  

You can put a post-ban upper on a pre-ban lower.  

You can alter a post-ban upper to have "evil" features, just don't put it on a post-ban lower.  An upper is not a firearm.

"M'kaaaaaaaaay?"

K, that is what I thought also.  
You can legally manufacture uppers now.  Pre/post -- so why should it be illegal to alter one.  
To me the complete package of the firearm is linked to the SN on the lower(pre or post).
The complete firearm is what adds up to the number of evil features.

Does anyone know of where I could get the muzzle brake removed?

ArmaLite doesn't normally sell "preban" uppers if the configuration, such as a mid-length carbine upper, is not cataloged as being available in "preban" configuration.  I managed to get a mid-length carbine barrel with no brake installed and the muzzle threads intact, but only as the result of a multi-step, major screw-up on their part.  They were trying to make me happy.

Kurt Walla of Kurt's Kustom Firearms on the Industry Forum can remove the brake for you.