As long as the fleetmate doesn’t have any timers (i.e. limited engagement, suspect timer), you can rep him without fear of picking up a limited engagement, suspect, or criminal timer.
Moreover, a green safety will protect you from suspect or criminal timers. So, feel free to try if you’re in doubt about something.
Finally, once a criminal act has been committed, nothing will stop concord from responding within the set time window (and anything that interferes with concord response times [outside the technique of concord pulling] is considered an exploit).
You might also want to check out the how to not be ganker bait section of this thread.