Please refer to the above image; this depicts a hybrid network of two different network capabilities, 1Gbps and 10/100Mbps. As long as the Gigabit devices are on their own "Gigabit arm" then they should be able to perform at Gigabit speeds with jumbo frames enabled or disabled. And the data transfers between Gigabit devices should remain within that particular arm only. If you observe that the Gigabit switch is sending data to the router, and then back to the other computer, then I would consider acquiring a different switch.
Devices should the 100Mbps network should work fine at their lower speeds, when they attempt to access data from the Gigabit side. Even if Jumbo frames is enabled, the system should auto-negotiate to use a lower speed, when communicating with the slower device.
Hope this answers your question