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It's a little unclear what the "latency issues" are. Are you saying there's latency issues when doing the backup or latency issues because of the backup? If the former, ever read or hear the late Grace Hopper's explanation of using satellite connection? The latter is often resolved with QoS.
Also if the former, backup impacted by latency, google BDP or bandwidth delay product.
Non jumbo frames support end-to-end shouldn't be an issue assuming there's L3 end-to-end as normally PMTUD would discover the maximum MTU end-to-end although having such support end-to-end would likely increase you backup transfer performance.
