Hi John,
I say go for it. I really like the idea of fighting fire with fire in the thistle counter attack you are planning.
One thing that comes to mind for me is the environment present when the thistle rust spores typically germinate and take hold - highest percentage of likely infection. I imagine it is temperature (high/low) related and some level of moisture dependent too. If you are familiar with the typical life cycle of that pathogen, even just from your casual observations, it might help you to emulate the proper conditions to get a take on the patches you are looking to really drop the hammer on. . . Worst case, the kill will be minimal, but if they are quoting a 45% minimum kill, perhaps it is quite straight forward. 45% is a pretty solid death rate for an organic approach and a step in the right direction, regardless.
I like the back pack sprayer approach.
You might even harvest a few batches of the dying thistle and keep it aside for spraying at an alternate time of the year, more inline with when the rust is naturally being released and plants are most susceptible . . . later winter, late spring, early summer, mid summer . . . you will likely know best, as you learn more about the fungal life cycle in question
Good luck and keep us posted . . . Love to see some before and after photos posted up here John!
Cheers
Gopher Hill ApplesZone 8 in California