I'm running off my SD card and I too go back to WM after a soft reset.
AFAIK there is no way to NOT get back to WM after the reset. The android program runs like any other program - except you can't exit out of it and go back to WM.
For me it takes at least a minute to go from the htc logo to the application start. And once i do get in I always get the "Process System is not responding" dialogue but I choose Wait instead of Force Close and then all is fine.
-P.