It is a bit difficult to know when you don't give us any idea what you mean by "large"...a "large" document to create on the iPad might well be much less complex than a "large" document created with the Mac, too.
Remember that there is no virtual memory system on the iPad, so OmniGraffle doesn't get a huge amount of memory to work in (and all iPad models are identically equipped right now). Are your embedded images sized appropriately for their use? Mashing a 16 megapixel image into a 300x300 box probably wastes a decent chunk of RAM, for example. Do you have lots of big stencils loaded? Do you get any better results running OG right after restarting the iPad?
Mailing a copy of your files that don't load all of their elements to
omnigraffle-iPad@omnigroup.com along with a description of the problem would be a very good first step. The OG team can use it to see if there is some optimization that can be performed (on the app and/or your diagram) to improve performance. As an additional experiment, you might make a copy of the doc with the embedded images removed and see how it compares. Not suggesting this as a permanent solution, just a way to explore the problem and perhaps get better performance while diagramming. My guess is that you can do the diagramming fine without the images, dropping them in after the heavy lifting is done, no?