Depending on the bullet and charge level, of course, the Whelan will produce more recoil energy than the .30-06. Whether it will bother you or not is another question.
The shape of the stock and weight of the rifle will have more effect on felt recoil than will the differences in recoil energy in either round. It will be possible to have a .30-06 that is less fun to shoot than the Whelan would be in another gun, or just the opposite.
I think your question is impossible to answer without actually shooting the gun and finding out the hard/expensive way. That said, I suspect that enough practice with proper technique would make that level of recoil acceptable to the vast majority of shooters.
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