If you’re using the Modbus binding, there are a number of ways to go about this. But your idea of exploiting REFRESH is good.
Configure your poller Thing for the longer period, then leave it alone, no need to disable.
Configure your periodic cron rule to optionally issue a REFRESH command. You only need to REFRESH one Item linked to that poller to get fresh data for all Items linked to that poller.
Actual update frequency of Item will still be limited by updateUnchangedValuesEveryMillis if you wanted to restrict update-to-same activity. Changes always passed.