Is it safe to toggle a led strip powered with 12v ATX PSU line?
This should be fine.


Generally the +5 V or +3.3 V line is accurately regulated and the +12 V (and -12 V, if provided) are relying on the turns ratio on the SMPS transformer to keep them in proportion to the 5 V supply.
Watch your current. The 12 V rails were only designed for hard drive motors which are not high power. The PSU label should give you the limits.