It doesn't deccelerate. The pcm pull timing to decrease the power output during the shift. It also pulls timing when accelerating from a dead stop. It is really bad in the 09's.
The Hypertech tuner should be out very soon (I am beta testing one now), but, as of now, it doesn't do anything for torque management. Dave at B&G can get rid of it, but that involves sending your box to him, him programming it, and then sending it back. He tuned one of my boxes before and did a good job. The only problem with going that route is that if you ever take your truck in for warranty repair they will know it has been reprogrammed.
As a point of interest:
There is a hidden code now (p2000) that comes up when you flash your box. I am not sure how long it has been around, but I flashed my 2000 many many times and it never happened. Every time I flash the 09 with the hypertech it comes up. It is clearable, but does not illuminate the CEL.