"Is it wrong to even associate with a company like Monsanto? What if they're providing some tangential support infrastructure that doesn't relate to the actual business practices that people are so ethically opposed to?"

Certainly. Ethics should trump finance in every scenario. There are very few companies as evil as Monsanto, and helping them further their cause is akin to direct involvement.

I see the nazi / ibm situation being tossed out in the thread, but in this case I think it's more like the RIAA.

Would you help the RIAA further their cause?