How to stop breaking SETA in X3 Terran Conflict?

By design SETA stops running the moment you press a key or move your joystick.

From the manual:

This extension is based on the phenomenon of the 
time and space anomaly observed in the presence 
of a singularity. The SETA is an attachment to the 
ship’s normal engines, which can, when activated, 
compress time up to ten fold. Due to the constraints 
of the space-time compression technology, it 
is not possible to alter one’s course or velocity. 
The device will be deactivated as soon as any 
interference to the ship’s controls is detected. The 
device was invented to shorten travel time across 
vast distances. No known side effects exist but 
they cannot be ruled out

Basically trying to control your ship under SETA would only smack you in to an asteroid faster than the onboard AI will. But if you use your onboard computer to plot a course through multiple sectors and gates, then you can activate SETA. It will have to be re-activated each time you pass through a new gate though.

BTW, welcome to the world of X3:TC, I hope you have a lot of spare time on your hands.