Performing a hard reset of the mobile device would fix the problem, but why should you have to hard reset your Pocket PC just to delete a Trojan? This equates to formatting your desktop PC every time you detect malware. It's an inadequate solution. Instead, use a process manager to kill the running application, and then delete it manually.
Performing a hard reset, does not equate to a format imho. Formating and re-installing can take quite some time, especialy if you have to re-install a hole bunch of software and configuration settings to get your box back to the way it was.

I was forced into a hard reset to day by battery failure. Took less than 5 mins to sync it back to exactly the way i had it set up. Mind you i would probably have had to take a while longer if i did not have a full back up.