Hello FC,
I guess the two choices are to use the timer channel to directly control the channel pin, or to use the timer as an interrupt only source, without affecting the I/O pin. It sounds like you require the second option.
With the direct control method, the interrupt latency does not affect the output waveform. However, with the interrupt only method variations in the interrupt latency will affect the pulse timing.
When driving a visual LED, small variations likely do not matter. For a non-critical 500 ms pulse, I would probably tend to use multiples of the timer overflow period to generated the pulse width timing, rather than a timer channel. Simplest operation of the timer channel occurs for pulse widths less than the overflow period.
Regards,
Mac