Lon, at this time throttling is available for the alternate mailing method, "internal PHP mail".
You will find some settings Delay "X" ms per message and "X" mins per "X" messages.
I would advise simply setting the first option, with the second set to 0.
A calculation might be
5000 messages per hour = 3600 seconds / 5000 = a delay of 720 ms
In a future update throttling will be more simple with a delay of X seconds (can be a 3 point decimal) per message. It will also be able to be enabled for both SMTP and PHP mail.
Regards