Filling holes in a timber workbench top
I would use a wood patch called a dutchman.
If your router has a plunge feature, make a small template to aid in cutting in a dutchman. The article the link refers to does it differently than I do, since it cuts out the damage and the  repair piece with the router using one template and two different guides. Where I use one guide only to cut the bad spot out, and a table saw or miter box, or sometimes both to cut the repair piece itself, depending on how big the repair is.

You would be able to get a dutchman in plane pretty easy with the surrounding material, but as with any repair of this nature, I would do it before the last pass of the router over the whole surface, then sand everything uniformly afterwards for the fine finish. This will clean up any glue mess from the install of the dutchman. 

The router speed to use on that is not critical, but for the larger bits, you can go too fast. Sanding will take out anything the router leaves behind. I would keep it a the lower half of your routers speed range 10,000 RPM max. The rule of thumb is, the larger the diameter of bit, the slower the speed. Some router bit manufacturers list the maximum speed a bit should turn. Other than that, listen to your router while it is cutting, its distinctive whine will change as it is pushed into the wood. Do not let it change in pitch too much. The amount you are cutting in one pass is a good amount, take no more on a full cut pass. As in each pass of the router cuts the full 1" width.

Learning to make templates and using bushing guides are one of the more handy things you would do well by.