I've got that same cooler on my board in my sig. Never noticed they were magnetic, to tell the truth. I can't imagine a little residual magnetism hurting anything when they are sitting right next to a processor that produces RF in the gigahertz range. It's not like they are close to magnetic media that could be erased. I use a magnetic screwdriver all the time on my builds to help hold screws and pick up dropped screws.
And the standoffs should not be sitting on any "circuitry". They should pass thru the 4 holes that the stock cooler passed thru.