I've flushed tranny's for at least 5 years... I have yet to see or hear on a real life experience were a flush has damaged a transmission. It is urban legend as far as I can tell. There is the possibility of a cleaner causing some seal problems, but I have yet to see that either. Although, I have only used BG's cleaner.
I have yet to see a machine that uses higher pressures then the transmissions pump is producing, so unlike many people think it's not really pressure washing the insides of the tranny.
The filter is a screen, so unless you have big tranny problems a cleaner and flush would probably clean out any debris that is in it. If there is much stuff stuck in the filter, a clogged filter is the least of your problems.
To me, flush is bad terminology. Everyone thinks you are using high pressure to push out the fluid and clean the tranny. I prefer the term fluid exchange. Because all you are doing is replacing all the old fluid with new. The cleaner will be completely out of the system with the 12-16 quarts of new fluid pushed through, so you cannot even argue that it may stay in the system and cause break down.
Keeping old fluid in there will cause more problems. The fluid lubes the inside of the tranny, there are bushings, bearings, gears, etc... that all need clean fluid to keep the lubed without damage. All new fluid will be better on those components then used or mixed used and new fluid, no if's, and's or but's.
I'd personally would not hesitate to have any local lube shop do it, if you want to be cautious, tell them no cleaners or additives just normal DEX/MERC III fluid like they will be using anyways. Or if you are really paranoid go to a dealer that uses BG equipment and chemicals, most new car dealers probably are BG dealers, at least here they are.