I prefer to try digging thistles from any landscaped bed and herbicides are a fine option as long as you're careful. I like the paintbrush idea, certainly less risk than my spot spraying. I've had thistles get bad enough to warrant digging the entire plant (daylily or other) to remove them. If I had thistle issues right now during the bloom? I'd just snip them off around an inch high and deal with them later.
Enjoy the bloom season knowing your thistles are suffering.
