Bitcoin from coinjoin can be and would probably be seen as tainted by exchanges, any coin linked to illegal activities are tainted.
Bitcoin from coinjoins, or bitcoin known to be associated with silk road 'type' places?
Yes
What if someone fed up with not being able to offload their tainted bitcoins send small amounts of theirs to public addresses that have lots of bitcoin.
Never use a centralized exchange. Or split the coins and send in like 5 to 10 different transactions to address you owned and split it the more, wait for like hours or even days before each transaction, the longer the better.
Would doing that, taint those larger addresses if those whales then sent their bitcoin to an exchange like Coinbase?
Coinbase is a centralized exchange and the coin will be seized and ID documents will be required.
How does it work, do these exchanges treat every wallet connected with a tainted wallet as also tainted or do they treat them as separate individuals?
No. Addresses. But it is possible that many addresses can be connected together. Another is a centralized server of a SPV wallet linking many addresses of the same wallet together and also with the IP address used.
Do not get yourself in anything that is illegal, this is just a means to avoid your coin to be seen as tainted.