We once had to do that and used JSS ID ranges, like JSS Computer ID is greater than 0 and less than 51 (to capture at most 50 Macs), and another group from JSS ID 51 through 100 and so on. Its a pain, no doubt. It would be a welcome feature if the JSS had a way to slowly increase machines into a Smart Group instead of all machines that fall into the criteria at once, or some other throttling controls for policies. For what its worth, policies are already kind of throttled by way of the random delay that occurs, so even if 100 Macs all decide to check in at the exact same time, they are all going to end up running the policy at slightly different times because one may run it after only a few seconds delay and another may wait for several minutes before finally executing the policy.
You could also look at setting your check in time higher, like bump it to 30 minutes with a 15 minute max random delay. That should spread things out a little more and help satisfy your network team.