Shoes are the most cumbersome thing to carry on a bike commute. If you are able to leave them at work, your commute packing will become 50% easier. I keep a pair of black & a pair of brown shoes at work & just change once I get there.

If leaving them at work is not an option, the rest depends on what else you are carrying. you can try packing them at the very top of everything so that nothing is pressing down on them. Also, as suggested, strap them to the top of the bike rack separately, or put them in a separate compartment of the backpack.