This really depends on your workload.
Interrupts
When the OS talks to the NIC (sending) or the NIC talks to the OS (recieving) it usually does so on a per frame/packet basis. Just imagine everytime your NIC recieves a frame/packet it invokes the OS's interrupt handler which usually requires two full context switches each time (one into the handler and one out of the handler).
MTU
The MTU sets how large a frame/packet sent on a network interface may be. This is usually set to 1500 bytes which is what basic Ethernet guarantees. Everything larger than this is called a jumbo frame. Even when you enable jumbo frames every frame will be just as large as required (i.e. the MTU is just the upper bound).
Increasing the MTU will require support from other components (i.e. switches and routers) and might increase the load on these components (e.g. IP fragmentation).
Advantages of Jumbo Frames
When your application sends large chunks of data, it will be cut into frames/packets and the interface MTU is the upper bound for the size.
It is, of course, preferable to have less frames causing fewer interrupts which in turn will lower the amount of time the OS will spend on interrupt handling.
However, this is only true if your application sends large chunks of data. While enabling jumbo frames will usually not hurt performance, it depends on your kind of workload wether or not you will see a significant improvement.
Conclusion
Jumbo frames won't usually hurt the OS itself.