It's not like the end of the world since you can do much of what the trainer does via the in-game console commands. Not as simple, but still functional.
I just hate having to pause every five seconds to spam health poultices.
runscript pc_immortal
Problem solved.
Surprise?
The trick is not to patch until the trainer is up to speed, obviously.
Well, it depends on the contents of the patches...
BTW, yesterday I finished the game without the trainer, and it wasn't so much of a problem, thanks to the uber stats (1000+).