Love the way that turned out in the Snickerdoodle!
Could you make a couple of felted flowers to put over the holes? Perhaps like the ones on one of Marnie's hats, then just felt them? Knitwhits.com has some patterns for knitted flowers and they come with felting instructions, too.
My crafting motto is "better done than perfect", so I'd make the holes work for me some way, some how!